Welp, I'm gonna say my thoughts for final smashes in SSB.
I always thought it'd be nice if you could have 2 choices in final smash. A transformation and an attack.
B would be the attack and B Down would be the transformation.
This way you could choose the final smash that fits the occasion.
For example: Mario's FS is an attack, as well as Luigi's and Pikachus.. Wario's and Bowser's are an transformation. I define transformation as a a invincible or near invicible transformation of a character, who keeps their moveset to keep fighting. So Pikachu or Game and Watch would not fall under this category. However under the circumstances of a few characters, their SF's would need to be tweaked a bit to be quicker and more dangerous making their 'attack' SF an actual single attack.
I'll use a few characters as an example with the new SFs everyone gets.
Mario:
Attack: His ol' Final Smash from Brawl.
Transformation: Eats a Mega Mushroom, grows huge! He moves slower and attacks are slower, but are much much more powerful.
Bowser:
Attack: Fires 5 fire blasts from his mouth, similar to http://youtu.be/Ihei0ngHHdU . However these are fired in a rapid succession and travel very very fast. The blasts, when hitting a player or obstacle explode in a decent radius doing the approximate damage of 2 bomb ombs.
Mega Evolutions just feel like a Pokemon only thing but imagine a mega evolution coming out of a pokeball. As long as there is a way to balance Final Smashes then I would say SMFs idea could be neat. Transformations (B button) are for giving damage out to people with low percents while the finishing moves (A Button) are instant kills if aimed right.
From Jigglypuff's Rest in previous games we know not everything Pokemon is going to be accurate in SSB. You could do that but don't expect using a mega evolution at the start of the battle. The closest it's gonna be is a final smash if there is a Pokemon that is playable and can do that. I'm sure Miiverse people already thought of that, but I don't think it's likely to happen.
I would think instead of having them transform and then go all-out, have them do like a small range attack and then transform like what Samus does. Then another smash would be a complete out-of-the-park-there-goes-the-neighborhood, followed by transforming back.
Like say Mewtwo would go into it's ball and do a psy-blast, transforming into the Fighting type form and focuses more on melee attacks. (ex. Mewtwo's regular special would be like Lucario's Aura Sphere, Mega form would be Focus Punch or something.) Transforming back would be, Idunno, using it's psychic powers to draw people close to it and then a powerful punch before transforming back.