I had a hard time getting into Paper Mario for that very reason as well, but once I did, I really enjoyed it. Thousand-Year Door is pretty much the same thing as the first, but it does it so much better that I love it as well. My biggest complaint with the Paper Mario games is the characters. Unlike in Mario RPG where your teammates were fleshed and actually characters, like Mallow, who's trying to find his parents, and Geno, who's a heavenly being trying to repair the Star Road, the teammates in the Paper Mario series are just devices. They exist only to perform a single action, and a lot of those are repeated by carbon copies in the sequel: Goombario/Goombella=information, Kooper/Koops=shell toss, etc. They aren't characters. They just do stuff. And while I like that from a gameplay perspective, it lacks in the story department. Also, it seems nearly every sidekick in the first two games are just reformed enemies. That seems to be a problem with a lot of modern Mario games where they've run out of ideas for characters, so they simply start turning all the bad guys into good guys, unlike Mario RPG that actually created new, unique types of chracters to interact with. Again, I love the games, but that's my main complaint. Super Paper Mario alleviated this by having the characters be established Mario characters: Mario, Peach, Koopa, and Luigi, while relegating the Pixls to gameplay devices, except for Tippi, who actually does have a character.
As for me, I love the Mario & Luigi series, even though I've only played the first (don't have a DS). It's nice to see Mario and Luigi function as a team and as individual characters, when the modern staple is to have Luigi either absent or functioning separately from Mario. It reminds me a lot of the old Mario cartoons I grew up with.