It has glitches (and so does Vice City; I just had it freeze on me on a level 11 vigilante mission...argh...), some missions are a bit connect the dotish, but after GT3, the two GTA games have become my favorites.
For one, the non-linear play, all the extra stuff to do around the cities is much different from other such games I've seen. And there're several ways to complete most of the missions, so you can see how inventive you can get, too.
And, both games are absolutely hilarious. I think this is what much of the more moral criticism misses. And, I do think, if someone's not mentally mature enough to get the jokes or that everything is a joke, then they really shouldn't play these titles. Without the humor, this would be a much different game.
But I may play it differently than most people, too. I actually avoid killing peds or police. Maybe I'm just nuts.
Anyway, I bought a PS2 specifically because of Gran Turismo, and after that, nearly everything else has been disappointing (but it did set an awfully high standard), with the GTA games being one of the few exceptions.
So, yeah, it may be overrated, but it's still a great game.