What I would do may look different to yours, and these changes are separate to their more in depth balancing nearer to the end of development which would sort out smaller things like hit box sizes, powers, frame data etc.
Mario: F.L.U.D.D. does a little bit of damage, and in the air becomes a downwards squirting hover nozzle, aiding vertical recovery and being a great gimping tool.
Luigi: Poltergust down-B, kind of like Dedede's neutral-B? I'm not sure, but he should have it. And a different Final Smash, either using it or backfiring it to release a bunch of boos and ghosts to attack everyone.
Peach: A final smash based on Super Princess Peach, with various mood swings causing different effects and finally calming down which heals her by a small amount.
Bowser: Yeah, they've kinda done what I would, though I'd consider making a tap of B shooting a fireball, and give Whirling Fortress projectile reflection, and maybe some more Armoured moves; all that depends on the balancing stage though.
DK: A roll dash move that be jumped out of into attacks. Rambi for final smash.
Wario: A shoulder charge side B. I hate that motorbike!
Link: Ho boy! More recovery, better defensive play with faster/better spacing using his projectiles. Normal Boomerang again, possibly with a slight stun effect like in his home games. There's likely more that would come up in balancing too. A Rolling bomb and Sword Beam on one of his moves would be nice too for even more variety in spacing. Lightning Enfused Skyward Strike could also work as a Final Smash, though I kinda like the Triforce Attack (but only once).
Zelda: Make Farore's wind more of a Teleport move, where you set the point and then when you use it again appear there. Perfect recovery, but the waypoint only lasts a set time before dissipating, and goes if you transform. Make Din's Fire bigger, more powerful, faster moving, and have the explosion linger for a while. Make her a bit heavier, though I like her being floaty. Then get onto more refined balancing, which I guess I'll have to fluff.
Ganondorf: Give him a projectile for neutral B, slight homing, chargeable but splits into multiple projectiles rather than one big on. They can be hit back with more powerful attacks and will target the nearest enemy. More an approach, pressure tool than powerful. Up-B being levitation and making him hover for a while afterwards if up is held, peach like (but weaker) air control during this helping his recovery be less predictable. A touch more speed is probably for balancing, but I kinda like him being slow.
Toon Link: A new final smash: a Hurricane Spin which can be controlled all directions hitting people multiple times as he hits them with great damage and knockback.
Samus: Stronger, faster charge shot so she has a killing move again. Bomb Jumping or Space Jump with the Screw Attack so she has better recovery. Sleaker movements, and slightly faster. A Lethal Strike down throw for a more local killing move. Final Smash stays the same.
ZSS: Other M design. Can switch into PSS with a taunt input. Final Smash is Crystal Flash with a full heal effect and some flashy push against foes, still puts on suit though; it's a cool gimmick. I would like to make her less laser whip reliant too, but I can't think of how to.
Pit: Already done.
Ice Climbers: Slightly dumber AI, but not as dumb as Melee, partly for 3DS, and partly for easier Nana seperation. Make Desync grabs harder (but not impossible), though I don't dislike the other attacks desyncing as that is their shtick.
Kirby: Implement and balance copy abilities better!
Metaknight: Copy Project M!
Dedede: Improve the Waddle-Dees and Doos attacks, speed and survivability. Possibly make Gordo slightly more powerful. Consider making Bandana Dee a possible, though very rare, throw, with some really powerful attacks using his spear (unless he's an Assist Trophy). Make chain grabbing a little harder?
Olimar: Add Winged and Rock Pikmin. Rock Pikmin have shield breaking capabilities while winged Pikmin fly straight forward when thrown for a log range. When a Winged Pikmin is at the end of the Up-B it will fly up a little way, helping recovery further. He shoudl have far weaker normal attacks though, relying far more on racking up damage with his pikmin! Purple smashes should be the only real killing moves in his arsenal.
Falco: Arwing Final Smash. Maybe a little more decloning, but I'm not sure he needs it, or what direction I'd take it.
Wolf: Wolfen Final Smash, or possibly have Star Wolf appear and fire with Wolfen.
Pikachu: I hate Volt Tackle. It doesn't look anything like the volt tackle of the anime, the animation of the game or the Volteccer of Pulseman... I'd probably make it more like the latter,
Pokémon Trainer: Get rid of the stamina gimmick. Change the type effectiveness so Squirtle and Charizard are weak to electricity and Ivysaur resists. Make it such that getting hit with an attack that they resist (ie. Ivysaur hit with Grass, Water or Electric) powers up their STAB attacks for a while (call the effect Torrent, Overgrow and Blaze).
Charizard: Rock Smash should be removed for Wing Attack or something move useful in FFA, and less broken in boss rush. Aerial Grabs with their own throws (including a seismic toss style animation). Boost the aerial game like Project M, but with air grabs. Also make Flamethrower while Gliding a thing.
Ivysaur: Bullet Seed for Seed Bomb/Leech Seed, which does damage and seeds the target making them heal Ivysaur slowly. Add (f-tilt, n-air) and edit some bulb attacks to include various powders, which will either stun for a short period (likely), poison (medium) or put the target to sleep (unlikely). Non-Mashable Jab, with more power. Other changed to help defensive play.
Squirtle: Water Gun does a little damage over time. Skull Bash for forward smash. Smallest changes, though some balancing will probably be needed.
Lucario: Mega-Evolution for Final Smash.
Mewtwo: ALOT! A little more weight, though still floaty, slow fall when holding up or possibly more jumps. Non-mashable jab, with more push back. Psycho Cut as an F-tilt? with short range pseudo projectile (that isn't counted as a projectile for reflection purposes). Psystrike as down-B, a powerful close range attack with a command grab. Kinesis as a tether grab, without/with less of the end lag. Confusion should have the best of both worlds reflecting projectiles and lightly dazing enemies (and turning them) much like Disable used to. Mega-Evolution for Final Smashes, choosable when you pick Mewtwo on the menu.
MegaMewtwo Y is smaller very fast and controllable in all directions, with use of Mewtwo's powerful aerial attacks and powered up specials.
MegaMewtwo X is even taller but still fast, with a high jump and fairly quick fall as well as extremely powerful aerial and smash attacks.
Jigglypuff: Pound should be replaced with a fairy move. I'd like to see Fairy Kiss is she gets access to it, so she has some sustain. It should still have some recovery effect if used repeatedly mind. There's a vast amount of changes for other balancing too, Rest should be more powerful too, and have some healing effect for even more sustain (it's a healing move in it's home game), and Sing should have a slightly bigger effect radius. Other balancing buffs would be needed too. Moonblast for Final Smash? Again, without the game released I don't know what Fairy moves she has access to.
Ike: A touch more speed, but not making him super fast.. he's powerful as it, but a touch too sluggish.
Roy: Only bring him in as DLC. Make his neutral B a fiery ranged attack based off his ranged attack in his own game. A glyph appears on the floor infront of Roy, getting bigger as the attack is held; and can be moved along the surface in any direction. I'm not sure how I'd balance him after that, but he should have a ranged attack!
Lucas: PK-Freeze for side-B like Project M. Consider Offense up for neutral-B, but I think I'd just make a faster, less powerful PK Flash than Ness. PK Wall as a melee counter for down-B, will counter with the damage and knock back Lucas would have received, while Lucas takes 50% of the damage, and none of the knock back.
Sonic: A Boost move for side-B. Faster attacking speed, for better hit and run.
Snake: Get rid of him! He doesn't fit, and Konami don't support the Wii U so they don't deserve a rep.
No F.L.U.D.D New Down special move To Super Mario Galaxy Like Mario Tornado
