People are upset by a few things it seems. PSN having a rough start up, weird errors, or ranked mode not working correctly. Super meter bars are shorter in some cases, making it harder to tell when your meter will fill up. Some sound glitches occur with GGPO rollback that causes the sound to stop. Also the PS3 has 2, maybe 3, frames of input lag. That's not surprising because PS3 games have been like that, but having certain sticks or tv setups can compound the issue even further. Apparently the 360 feels more like the arcade and the netplay is smoother on the initial day. Definitely a lot of people mad saying it's not arcade perfect and various other things. It was bad enough that someone from Capcom emailed/called a well-known arcade owner who was streaming his local battles with friends because they kept trashing it because of the input lag.
If you're wondering what version to go for, might want to lean towards the 360. You may or may not notice the input lag depending on some factors, but it may be worth it just to go with the 360 just in case.