I don't mean in terms of controllers. I'm wondering if one of the versions has any glaring flaws (framerate issues, worse online stability, other bugs), or if the versions are 100 percent comparable?
I wish I didn't have to ask but it seems like alot of games that comeout one of the systems has flaws of some sort.

I've heard nothing about issues on either platform. It wasn't ported (from what I know), so it should be fine on both. 
 
PS3 has a great fighting-game community on GB.

Whatever your friends will be playing on. 

Yeah, I'd check out the community threads and see which one caters to your playtimes more. But overall it seems like the real MvC3-heads that have been jawing away about theory and shit on these forums are PS3 players.

Both have strong communitys 
 
PS3 
 
360 
 
The PS3 community right now seems much smaller then the 360 one. 

" @The_Laughing_Man: Lots of names of a list is not equivalent to a strong community. "

" @GetEveryone said:

" @The_Laughing_Man: Lots of names of a list is not equivalent to a community. "

I never said " Strong" I said smaller.  "

I got mine for PS3 because of the controller. 
 
D-pad is doable on ps3 but nothing for me on the 360 controller worked 

" I got mine for PS3 because of the controller.  D-pad is doable on ps3 but nothing for me on the 360 controller worked  "

" @The_Laughing_Man said:

" @GetEveryone said:

" @The_Laughing_Man: Lots of names of a list is not equivalent to a community. "

I never said " Strong" I said smaller.  "

Amended. "

" @The_Laughing_Man: Yeah, I didn't mean to start an argument, mate. Apologies for the snarkiness.  We actually don't add names to the PS3 list, though.  The point in that thread is for people to add the regulars, so that they are guaranteed games. If they play a lot, they get added to it. It's a means to prevent the list becoming a mess of people who posted their details once and were never heard from again; as was the case with the S/SF4 match-up threads. "

I'd say PS3, but that's because I'm biased. So far as I know, the two are pretty identical technically. 

i experience some chugging in the framerate on the 360 when the fighter does his/her little win pose after a fight.  Only on some of the more detailed backgrounds.  Don't notice any framerate issues during fighting tho.
 
Matchmaking-wise on the 360...I can seem to only get into games if I go to Lobby Search.  If I try to join a ranked or player game it just says I lost connection to the host.  Sux for now but it will be fixed I'm sure.
 
I'm using the adjustable D-pad on the 360 controller.  Works a bit better than the normal D-pad that just a flat circle.