San Andreas has the best story and most features but it needs updated. It has so many little things like stealing from peoples houses while trying not to wake them up or adding hydraulics on your car and competing. Those little mini games could certainly stand some better treatment to make them more robust. Hell bring back the sex mini-game, it was actually pretty tame and it's not like it showed anything hardcore but rather more like soft porn if that. Of course such a remake will never happen within the next 20 years but I'm sure it would be a huge hit if they did.
I'm curious where the next GTA will go. I'm thinking they may try to tackle the 50's or 40's or even 30's era since there was a lot going on in the crime world in those days and it's a ripe time period for a GTA. However as far as parodies go I think many prefer the modern era since it's something we can get and follow. Any parody of history would likely fly over most gamers head.
What would be cool is if they could use Google World and try to simulate that down to more street level detail but that would require a ton of algorithms to pre-generate stuff to a better level than suck.