That's pretty much what I was getting at with them being like the chests -- they're only there to fulfill arbitrarily necessary gameplay mechanics, and to be funny. You worded it better, though.
Paper Mario and Thousand-Year Door did a great job making a real coherent world, making characters feel like actual people with fears and aspirations, and being genuinely endearing while maintaining a great sense of humor. The Mario & Luigi games, probably by virtue of being a handheld series, tend to dispense with any seriousness and just be funny. There are no real characters in Superstar Saga -- pretty much everyone is just a one-off gag in the ongoing slapstick routine. Like when you get the S.S. Chuckola into the water and it floats for a few seconds, with the captain jumping for joy up on the deck, and then it hits a rock and sinks -- from that moment on, the doors into the ship are permanently shut and you never see any of the crew members ever again. All those people are trapped in there forever, and the game doesn't even pretend otherwise. I'm supposed to just laugh and move on, but I just felt really bad for all of them.
(Incidentally, SMRPG didn't do that. Almost every character shows up later somewhere or gets visited again -- Raz and Raini, Booster, Valentina, Johnny, Belome, Knife Guy and Grate Guy. Most of the characters that don't -- Monstermama, Hinopio, Ma and Pa Mole -- at least have the decency to stay in one accessible place so you know they're still alive. The bosses, being robotic weapons, show up again in a sense when we find out that they were prototypes for mass production. The only characters who are kinda like Mario & Luigi characters would be Punchinello and the random unexplained bosses in the rushed endgame -- Cloaker, Domino, Count Down, Gunyolk, Clerk, et. al.)
With Super Paper Mario, a little bit of the comedic sadism (or at least misanthropic detachment) of the Mario & Luigi series started creeping in. Not that there's anything wrong with Mario & Luigi, but there's a reason there are multiple serieses. I hope Sticker Star can keep the empathy of the Paper games. Having partners is a really good way to do that, but if they can do it another way, I'm up for it.
I really want a Paper Mario game on the Wii U, though.