A few players commented that the Marvel vs. Capcom 2 select screen was different than the arcade release, and the game's producer, Rey Jimenez, stepped in to cover that subject on the Capcom Forums.
In the arcade version and console version of Marvel vs. Capcom 2, some characters were in different places on the screen, like Magneto, why is that? — Nadino
It's because they're unlocked in different orders. So you'd have one set of default characters in the arcade, and one on your console. — Preppy
Rey: As Preppy said, it has to do with the unlock order. The character slots unlock in a specific order. I wasn't on the original Dreamcast game, so I don't know why the change from the arcade to Dreamcast, but I can comment on why the change from the Dreamcast to the 360/PSN versions.
For the demo, we wanted to have 6 characters available. Because of the way the game unlocks characters, they needed to be in the center six. The six characters there by default where not the characters we wanted for the demo, so we had to do a little rearranging. Because the demo is actually the full game but with demo specs applied, the character mapping remains a little shuffled for the full version.