The control scheme is an important part of any game and can affect the smoothness of play or add fake difficulty if done poorly. Sadly, control schemes are rarely given much thought or appreciation by gamers.
As a person who thinks about control schemes a lot, I have a few issues with some of the controls in MKF so far and I have some suggestions. Those marked with IMPORTANT indicate conflicts in which two moves are assigned to the same button combination, with one replacing the other.

GENERAL NOTE: Platforming controls and combat controls should be kept as independent as possible, especially in a game that mixes them like MKF.

MARIO/LUIGI:

* Fireballs, Hammers, Boomerangs, and Busters should be moved from the Run button to the Shoot button.
Reason: This allows shooting while running without losing momentum. Attacks that break momentum anyway, like the Tail Whip and Spartan Sword, can be left on Run.

IMPORTANT: The Slide should be moved from DOWN + Jump to DOWN + Run.
Reason: The Slide currently replaces the crouch jump. DOWN + Run is the best alternative because it is similar to a running crouch, the alternative to sliding with other powerups.

SONIC/TAILS:

IMPORTANT: The Spin Dash should be moved from DOWN + Run to DOWN + Jump.
Reason: Tanooki Tails' statue move currently replaces the Spin Dash. DOWN + Jump is the best alternative because it is the Spin Dash command in all 2D Sonic games.

IMPORTANT: The Fireball Spin Dash (Fire Shield/Kevlar Shield) should be moved from Jump in midair to Shoot.
Reason: The Fireball Spin Dash can currently interfere with Tails' flight. Shoot is the best alternative because it is currently only used for the Mega Man suits.

* The Fireball Spin Dash should be usable on the ground.
Reason: The Fire Shield is a bit boring and will be even less appealing once the Protection Crystal becomes available. Since it's essentially an instant Spin Dash, it wouldn't really increase Sonic or Tails' abilities at all, but it would make the Fire Shield more fun.

LINK:

* The Sword should be moved to Run and projectiles moved to Shoot.
Reason: This allows shooting while running without losing momentum. Since the sword already arrests momentum, it should be put on Run.

* Zero Link's Super Slash should be moved to UP + Release Shoot. Releasing Shoot without UP should result in a projectile attack.
Reason: A projectile attack turning into a melee attack when charged feels unnatural. The Blade Armor in Mega Man X6 had a charge attack that turned into an enhanced saber slash if you held UP when releasing the charge, so it makes sense to use the same button combination here.
EDIT: Zero Link's Saber and Buster now charge separately. This is no longer an issue.

GENERAL:

* The advanced swimming controls (hold UP while swimming to surface quickly; hold DOWN while swimming to float at a constant level) should be explained in a Help Box in-game.
Reason: Having watched several Let's Plays of MKF, this is the single issue that causes the most grief. The advanced swimming controls are pretty much required to get through most water levels, and most players don't realize they exist.

I may have the artistic ability of a roadkilled slug, but control and mechanics are what I'm really good at. This is the only way I can contribute to the development of MKF, and I want to be a part of this. If you have a problem with any of my suggestions, please explain why.

What you're suggesting is reasonable, but would take an awful lot of recoding. I know I don't want to do it, and I'm sure Obreck doesn't want to do it either. So I'm not sure what to say about this.

Bravo.
Many a death because of those issues.
While certianly not game breaking i feel that some of these make sense.

Though others. Like the Zero link complaint don't really make sense.
I mean have you even played Megaman X3?

And then theres shodain's argument which i wholeheartedly agree with. Game maker isn't exactly a cake walk as we all well know.

I agree with shodian.All your ideas are complaints
that i've had,Just never brought them up.

It would be nice to see them fixed,But I'd much
rather see them spend time on Samus Or kirby
rather than using their tiem to do this.

After all,Despite the annoyances in the control scheme,
Mkf is still playable.It can just be annoying in moments
where you need to think quick and automaticaly
press the button that makes the most sense,Doing the wrong thing,
And thusly killing yourself. >.>

*agrees with Shodian*

Programming is difficult, reprogramming's even harder. Trust me, I know.

I'm not saying this should be done right away. I'd just like people to keep these in mind as development continues. Maybe if the controls need to be reprogrammed for some other reason later, these changes can be slipped in at the same time.
That said, I would like these to be implemented before the final release, and the earlier they're implemented, the easier this will be (I assume).
By the way, it's good to hear that other people agree with me. It makes me feel like less of a crackpot.

Well our main concern is to finish the game, and once we do, then we can turn to these minor matters and attend to them. But for now, they work, that's good enough for now.

Excuse the necropost, but I have some new, relevant information:

Perhaps the argument yet for changing the Spin Dash from DOWN + Run to DOWN + Jump.

Besides the the issues with intuitiveness and Tanooki Tails, we now have concrete proof that the current control scheme is messing players up.

Remember, the sooner we change them, the easier it will be for everyone!