Chrono trigger wins, but Paper Mario 2 is more fun imo. I just looooove chapter 3. Everything about that chapter was just so immersing. Mystery, battle, rising action, suspense, climax, and just pure win.
Seriously, the humor in Paper Mario 2 is great. I love the little jokes they throw in. The characters are well developed too, with a unique prepared response for every one of them in any partner speech. I love when Professor Frankly is says something like, "You're marvelous!
Terrific! Wonderful, even!"
Actually, when I first started playing that game, I was shocked by how mature and morbid it was for a mario game. Starting in Rogueport, if you read between the lines in Goombella's descriptions of people and Rogueport, it's crazy how many suggestive themes are in the game. She identifies hitmen with fancy language that only an adult or older teen would understand. Early in the game, Mario and Goombella are attacked in a mock sexual assault. Serious stuff. It made the game a lot more real to see aspects of reality in it. Vice, gambling, crime, thieving, gangs, graffiti, murder, mafia, street fights, sexual harassment, etc. (Phew, no prostitution.) You just don't see that in other Mario games, where the world is perfect, save Bowser.
...Well, OK, sometimes there's casinos or thieves, but never this many forms of vice thrown together.