I like them both the same for different reasons. Like some people have said, it became a parody of itself in SR3. It just got wackier and wackier over the course of the game, which is great and fun. But SR2 was at least somewhat grounded. And The Boss was a bit of a ***** in SR3, he was just a murderous psychopath in SR2, who wouldn't take shit from no one, but he just seems to roll over and take abuse in SR3. Saying that, Co Op in SR3 is some of the best fun I've had in a long fucking time.
Although I hated how Shaundi was changed in SR3, she just wasn't the same character anymore. Like at all.
I will say though that I don't think it's fair to compare SR and GTA, they're too divergent at this point, and I think GTA 5 will be great, as I think Rockstar will take what they've learned in writing Red Dead Redemption and LA Noire to make a really compelling story, GTA 4 had some real glaring narrative pacing issues, but hopefully GTA 5 will improve on that. There's just no point in Rockstar trying to make a silly sandbox crime game anymore, Saints Row has that covered, so they might as well go the serious route.