Depends if we're talking mainstream or not, though you seem to want to go with that safer answer.
GTA is only controversial through the news media using it as the poster child for everything wrong. If you actually examine the gameplay and the story, it's no more controversial than, say, Sleeping Dogs or Mafia II.
You're probably closer to the mark with the first Manhunter game (still wish devs would use that talk-to-you-through-the-microphone trick again).
This gen there's a game that should have been more controversial than it was, probably because it was such a bland and boring game. Call of Juarez: The Cartel.
Also, how do we define controversy? Something that garners negative press? Because lots of games have managed just that. Dante's Inferno, for example, got negative press from EA hiring a bunch of fake protesters to pretend they were christians rallying against the game. Or the devs from Homefront that released all the red balloons that ended up in the local river and all over the countryside when they deflated, creating litter.
My friend and I were just talking about this, so I figured I'd ask you guys. I said either Postal or Manhunt, while my friend said the GTA franchise.
When I read the topic title, Manhunt came to mind. There have been many though. Doom was a big deal in the early 90's, GTA was controversial but it seems to have calmed down a bit as people have accepted video games as a form of entertainment for all ages.
I *think* it was the first video game to be banned in the UK. I remember the news reports, BBC got a gamer on to be interviewed about it. He was the prototypical 90s gamer with glasses and spots and everything. Skinny too, because we only learned to be fat once we got older.