I'm experiencing something similiar. My PS3 controllers only work when they're plugged in with a wire when trying to play this same game. Kind of annoying to have to sit so close to my TV to play it. Is this a common issue with PS2 games downloaded from the PSN or is there a bug in San Andreas?
I guess no fix to this has ever been found? My issue is that there is quite a bit of lag from controller input to execution of function, particularly when multiple commands are being made.
For example: tapping L1 will sometimes fire a single shot, sometimes it will fire no shot, sometimes it will fire ten shots.
Another example: When holding R1 to aim, pressing L1 to shoot and using R-Stick to strafe, the strafing action does not occur immediately when the input happens. It might be five or six seconds later that CJ finally rotates to the right. Makes it hell to shoot down helicopters.
Another example: Driving. Holding down X is already one input. Attempting to skid around a corner requires L-Stick and R1 and X again in rapid succession. Sometimes the car stops turning for a brief second and heads straight (into a building, cop car, losing a race etc) before suddenly registering the input from the controller again.
I think this all stems from the fact that they simply ported this game over to the PS2 without updating it at all. There's other PS2 games out there that have come over to the PS3 that have been updated to include new items, HD graphics, controls updated, everything but the essential story. You can't tell me that the makers of the GTA series don't have enough money to make a proper upgrade from PS2 to PS3 for what is arguably the best GTA game of the last decade.