That's a tough question really, because there are a few boxes that are ticked by different GTAs for me.
Story: This one has to go to GTA IV, easily. It really is completely unmatched in that regard, at least as far as other GTA games go. Nico is probably the best thought-out character they had. There really was no other character that had such personality and was this believable all around. He was a character you could really care for, if you wanted.
Plus, GTA IV is, of course, the best looking GTA to date and offers insane details if you're keeping an eye open while wandering through Liberty City. The whole city feels incredibly alive!
Athmosphere: This one would probably go to GTA III for me. Granted, that's a very, very subjective thing and I'm probably fooled by the fact that I was a lot younger when I played it, so nostalgia might come into play here. But still, no GTA has, so far, menaged to give me the same feeling GTA III did. Portland always felt so dark, so gritty, so rough - almost intimidating. I can't quite put my finger on why it was that way (or at least, why I remember it that way), but it was awesome. The only game that surpassed it was Red Dead Redemption...
Size: I don't really know whether 'size' is the right word here. But GTA: San Andreas was so huge! The thing I loved about it was that it wasn't only one big city, but that it also allowed you to explore the more rural areas and the desert and such. You could put stuff like the dirt bikes and such to good use. Also, I liked the RPG elements, even though they were very rudimental.
In the end, it's either GTA IV or San Andreas for me, but it's really hard to decide which one I like best... So I won't
