Since other people have made threads collecting their various suggestions for MKF, I decided to do the same. Here are some suggestions I've made or supported, past and present:

-Move all Mega Man weapons to the Shoot button.
Some characters have to have their Mega Man weapons on Shoot because of their control scheme (Arthur, Roll, Wario, Link), so why not just have it for everyone? The Mega Man weapon is usually some sort of projectile attack, so it's well-suited to the Shoot button. Plus, it's generally an added attack that doesn't affect the character's platforming controls, and the Shoot button was added specifically to be separate from running and jumping, so it's appropriate.

-Remove Mega Mario's recoil on the ground, but not in the air.
EDIT: No one seems to like this idea, so just get rid of the recoil entirely.
EDIT 2: It looks like recoil has been removed for 0.3.

-Move Mega Mario and Proto Luigi's slide from Down + Jump to Down + Run
There are two primary reasons for this. One, it currently replaces their crouch-jump, and no powerup should interfere with basic platforming ability, least of all the Mario Bros.'. Second, consider this: If you want to slip through a narrow space without the slide, you would get up a running start, then crouch just before you reach the opening. In other words, you would hold Run and press Down. If you do have the slide, you could just use that, which, if you follow my suggestion, would mean you would hold Down and press Run. So you see, there's a coherence with the button commands, and running and sliding are both movement abilities, so the command still makes sense. Hell, this way maybe if you screwed up the command somehow it might still work.
(By the way, I noticed in the latest Link video that Zero Link has a Dash now. Is that also Down + Jump? If so, this applies to him too.)
Roll's slide should remain Down + Jump, since she can't crouch-jump, and her slide is a bit different anyway, as she can use it to extend her jumps.

-Have Zero Link's fully charged shot normally be a projectile, and trigger his enhanced Z-Saber slash by holding Up as you release it
Again, two reasons. One, it seems a bit odd to me for a projectile attack to turn into a melee attack when you charge it, and it seems like that could throw players off. Second, this is how it worked with the Blade Armor in Mega Man X6: the fully charged shot turned from a projectile into an enhanced slash if you held Up when releasing it. Obviously, Zero Link's fully charged shot shouldn't be the same as Mega Mario's, as that would be too powerful, so I think that it should either be Blue Bomber Roll's fully charged shot or the same as his partially charged shot.

-Replace Zero Link's midair saber slash with Zero's spinning slash
I can't remember if I'm the one who first suggested this, but when it first came up it was shot down because Zero Link wouldn't have a midair slash, only the Up and Down Thrusts. Based on the first Link video, though, this was changed, so how about it? It wouldn't significantly increase Zero Link's power level, but it would be cool.

-Increase the power of Hammer Mario's hammers so that they can take out any enemy below a Gate Guardian in one hit
I talked about this a bit in another topic, but in case you missed it, Mario's hammers were awesome in SMB3, able to take out even Thwomps and Boos, and I don't think they're getting their due respect in MKF. The Hammer Suit is supposed to be a higher-tier powerup, and Mario's powerups are supposed to be more powerful anyway.

-Increase the range of Boomerang Luigi's boomerangs to be on par with the Boomerang Bros. he's copying
Again, this was addressed in another topic, but I'm gathering everything together here. Luigi's boomerangs currently have the shortest range of any boomerang weapon in MKF, which doesn't seem right when his powerup is named after them. Yes, you can jump over them coming back, but this is impractical in tight quarters, especially in autoscrolling levels, and in MKF the two tend to go together.

-When Arthur changes weapons, he should change instantly, rather than having to catch it as it comes down like a reserve powerup
I wasn't the one who came up with this, but I do support it, so I'm including it here. Weapons are different from powerups. Arthur isn't really gaining anything when he switches weapons, so why should he have to struggle for it? Arthur's all about his weapons, so when he wants to switch, he should get to right away.

-Sonic and Tails' spin dash should be moved from Down + Run to Down + Jump
This is simple: the spin dash has always been Down + Jump, even when the Sonic Advance series added a second button, and Down + Run is Tanooki Tails' statue. (I think this one may already have been implemented.)

-All characters should have looking up sprites, and Small Mario/Luigi/Wario should have crouching sprites
This just adds a little more character to the game, and shouldn't be too much work (you could use the code for crouching while running for how it affects their momentum). Mario and Luigi's looking up sprites should be based on their SMW ones, rather than that awful one from the SMB3 opening.

-Sonic's jumping while carrying/holding sprites should be separate from their walking animations
I know that the new Sonic skin is still a WIP, but from the videos I've seen of it in action, this sprite looks really weird. His legs in the jumping sprite should probably resemble his spring-bounce sprite.

EDIT: Forgot an important one:
-Sonic and Tails' ring counts reset to 10 when they earn a 1up instead of 0.
Currently, Sonic and Tails are completely vulnerable when their ring counts reach 100. Even if they don't get hit, having less than 10 rings disqualifies them from getting upper-level powerups. Both of these problems can be easily solved without significantly changing the ring system by just making Sonic and Tails' rings reset to 10. True, this would mean that they were closer to their next 1up, but the fact that they lose rings when taking damage compensates for that.

EDIT 2:
-Spartan Mario should swing his sword sideways when Spin-Jumping.
This would require a new sprite for the sword seen edge-on, but that'd basically just be a green line. This would basically be like Raccoon Mario swinging his tail when Spin-Jumping, only more powerful and in front of him instead of behind.

EDIT 3:
-Fireworks when you grab the flagpole at the right time, like in SMB and NSMB.
Obviously, this is just for fun. I was inspired to suggest this by the commentary on a really awful Let's Play.

That's all I can think of for now. Comments? Support? Criticisms?

Alot of these suggestions are either bad, or just plain unnecessary.

Megaman Firing on the Weapon Key: While it is a possibility, it's really the way it is because the fire flowers and all that work on the same principle.
With Arthur, it's different as his normal weapons include Robot Master weapons.
With Roll, she has a robot master weapon in addition to her normal buster shot, which gets changed depending on the suit she's wearing. Her normal buster uses the run button, as she doesn't run anyways. Her robot master weapon uses the weapon key.
With Link, he always has his sword which uses the Weapon key, which may get updated, depending on the suit he wears. In the case of the Zero suit, he has the beam saber, and then he has the Zero Buster, complete with the short ranged fully charged shot, which uses the Run key.
Wario, finally, uses the Weapon key to summon Guts Blocks for use of the Gutsman suit's Super Arm. Because of his complete lack of mobility, it was probably chosen to be placed there, as his only good way of clearing gaps, his dash, is pretty essential to him.

So yeah, unnecessary, I'd say.

Remove Mario's Buster recoil on Ground, but Not Air: Yeah, no. This is just rather pointless. The Fuel Rod cannon that Roll gets has an automatic knockback whenever a fully charged shot is fired, regardless of position. And this whole thing is really just a minor nitpick. Either the recoil is removed completely, or not at all. Who even gives a shit, honestly?

Move Slide w/ Mario Bros Megaman suits to down/run: Yet another minor nitpick. The slide/dash is very helpful, and I really don't see any really big reason to why it should be changed. No, seriously, stop yourself for a moment. Is it really that big of a deal if it isn't changed? No. It's not. It works fine now, and it will continue to work fine.

Various Link Related Suggestions: Are you kidding me? Before you even THINK about suggesting these little gameplay tweaks for Link, you should actually PLAY as him. Not watch a video and guess the controls. PLAY as him. Wait to the next public release.

Increase Hammer Bro. Mario power: He's already powerful. I don't see why he needs to be OPed.

Boomerang Luigi range: Now this probably has merit. I dunno, I'd have to see what the other dev's think about it. To be honest, I've never really used Luigi as much as Mario and most of the other characters.

Arthur Weapon Switching Time: I'd probably be against this, given that he is a TANK. The only possibly place where this would be explicitly helpful would be in an autoscrolling section, but even then, it's not necessary. GnG games usually revolve on getting the best weapon, or your favorite weapon, and just spamming the shit out of it on the enemies. In MKF, it's like that, although to more of a very lesser extent. The dagger rocks, the excalibur is goddamn awesome, and the golden axe is a monster. It's a small price to pay, really.

Change Spindash Button Combination: In Sonic games, the spindash was always on the jump button, but then there was only one real button. There wasn't a run button on Sonic games, as you would always move into top speed. Here, it works, and it helps you jump from a spindash. Live with it.

Looking up/Ducking in Small form: These are the most useless of useless of all of the things you can add to controls. None of them would help at all, as you really don't need to look up to see something, and you're already the smallest size you can be in small form. Don't see a reason why this is needed either.

Changes in sonic's skin: .....what?

The only suggestion I agree with here (and I don't even know if he meant it) is changing MegaMario's charging button to the third button, just to don't have it charging ALL the time, since when you play as Mario you need to have the run button pushed all the time, and it's annoying to be hearing that BEEPBEEPBEEP all the time and then knock back when you need to kill something as small as a Goomba.

And Luigi's Boomerang.

Okay, Xavier: Your main beef seems to be that most of my suggestions are "unnecessary". Does something have to be necessary to be added? If it will improve the game at all, then it should be put in, even if it isn't strictly necessary.

To respond directly to some of your criticisms:

Mega Man weapons: It's unnecessary, yes, but my point is that I think it would make the game more playable if there were more parallels between the different characters' controls, as long as it doesn't interfere with any existing moves. So, unnecessary, but beneficial.

Recoil: To tell you the truth, I just want them to get rid of the recoil altogether, but when I said that, the people who use it to extend their jumps whined. I came up with the ground/air idea in the hope of pleasing everyone, but if it's not going to please anyone, to hell with it. Just get rid of the recoil then.

Slide: Yes, there IS a big reason for it to be changed: it removes their ability to crouch-jump. And if you try to tell me that crouch-jumping isn't useful, then you haven't been playing enough Mario games (including MKF). Since there is a clear problem with the status quo, I'd say this change is necessary, not just nice.

Link: Okay, I'll give you that one.

Hammer Mario: He isn't actually all that powerful. The hammers need to be considerably more powerful than the fireballs to make up for them being so much more awkward to use. If it can't take out all enemies below Gate Guardians (which are the unimportant battles anyway), then it should at least be able to take out all the enemies it could in SMB3.

Arthur: It wouldn't significantly increase his power, it would just make him a little easier to play as.

Spin Dash: I told you, there IS more than one real button in the Sonic Advance games, and it's still on Down + Jump there. And there is a current problem with having it on Down + Run: Tanooki Tails can't spin dash because Down + Run is his statue. Because of that, I'd say this one actually is necessary.

Looking up/Crouching: This one is mostly based on Super Mario World. Obviously Small Mario/Luigi/Wario don't get any smaller when they crouch since they didn't in SMW. This one really isn't important, but it's a small change that's easy to make and adds a little extra charm, and it's the little things that can make the difference between a great game and a legendary game.

They've changed the charge sound so it's less annoying.

I agree that Luigi's Boomerang Bros. Boomerangs need more range, actually I was the first to bring that up, but Mario's hammers actually aren't too bad as they are now. They can take out Twomps and Twimps and do considerable damage to bosses. In fact I used the Hammer Bros. suit to beat King Watinga's Revenge and several of the Robot Masters. The only problem I have with it right now in MKF is it can't take out the Podaboos(sp?) like it could in SMB3, and I think it should be able to take out the urchins too. Everything else about it is pretty much good.

In JS' latest vid, he seems to have increased the boomerangs' range. Also, Mario still has the old charging sound, but maybe he hasn't implemented the new one yet.

Hey, where is this vid you're all talking about?