I just wanna preface my response by saying that one of the nice things about this thread is being able to have lively and civil discussions with reasonable people, so thank you for giving me that pleasure lol.
I should clarify the point I'm making. I am not arguing that a 2D fighter for indies couldn't work, or even that it couldn't work well. Rather I am making the case that the style of movement and combat in a platform fighter is much better suited to faithfully representing platforming characters, and is thus a better fit for an indie crossover fighting game.
The Mega Man example you brought up is a good illustration of this point. I'd say they did a pretty good job portraying Mega Man in Marvel vs. Capcom. In fact it's hard for me to imagine them doing much better than that in a 2D fighter.
So let's compare.
Here is Mega Man in Marvel vs. Capcom (all timestamped for you and ready to go):
Now here is Mega Man in Smash Bros (I would have used the super hype Mega Man matches from MLG last night but they aren't uploaded anywhere I could find yet):
Now compare those with some random gameplay from Mega Man 2:
If Mega Man looks more authentic in Smash Bros, that goes double for actually controlling him. When you play Mega Man in Smash you really feel like you are playing Mega Man from the original games. Mega Man in Marvel vs. Capcom is neat, but it's not the same. The fundamental reason for the difference is that Smash Bros provides an engine where Mega Man can move and attack platforming style just like he does in his original games, whereas Marvel vs. Capcom does not.
Don't get me wrong, I like your idea, and an indie crossover 2D fighter could be really cool. For the reasons above though I really think platform fighter is the way to go.
Oh and another important reason I didn't talk about before: we are in desperate need of more great platform fighters. There are already tons of great traditional 2D fighters, but as far as platform fighters go it's basically just the Smash Bros series and probably Rivals of Aether when it comes out. That's crazy. Platform fighter is such a great genre, and yet it's so under-explored. Seeing a big, innovative, indie crossover game in that style would almost be even more exciting for me than Shantae appearing in Smash.
I guess ultimately it comes down to personal preference, and I have no contention with you if you just happen to like the idea of a 2D fighter better. But those are my reasons for being all on board for a platform fighter instead.
EDIT: fixed the timestamps
EDIT: fixed the timestamps again (for real this time)