The netcode for MK9 was absolutely atrocious at first. With the recent patches there's barely any lag, but now it constantly desynchronizes.
And I'm amused on how morons online tell me to get a better connection and I try explaining to them that it's the necode and they still say it's my connection. That just shows total ignorance. Yes, it is true that a bad internet connection COULD be the fault, that's obvious. However, it's a pretty easy factor to rule out if you play other fighting games (and games in general) and you experience no lag on a consistent basis yet on MVC3 there is always that amount of input lag which is noticeable at best... I won't even go into what it's like if you don't get someone who's compatible.
With the recent patch for MK9 and SSF4 I hardly get lag, yet I get a lot of it on MVC3. My internet connection? In this case I don't think so. Couple this with the sheer number of people complaining about this problem then you can conclude that there is something wrong with the netcode.
I didn't even have this problem when MVC3 first came out and I'm using wired.