Yeah you duel the same way. There are tag battles now though, and turbo duels (which are stupid; the only difference is you cannot use Spell cards unless you have Speed Counters). Also, there's a new type of monster card called Synchro, which makes the old Fusion type completely useless.
Yes the framerate in the game does suck, especially during duels when the AI is thinking a lot. This is normal even in retail carts, though the lag in flash carts will be a bit more noticeable. I don't think it has anything to do with whether or not the game is patched.