My favorite game of the series is TTYD, followed by the original. For me, the original was a fun prototype, with the sequel being the refined, perfected end product.
I am not actually that fond of Super Paper Mario. What I like most about the Paper Mario series is that it takes all the nonsense that Mario has amassed over the years and weaves it into a coherent, functional world. The mushrooms and turtles and whatnot you usually just jump on actually have lives here, living in communities together, having jobs, doing things, stuff like that. This was at its height in TTYD.
SPM went away from that, focussing on a world inhabited not by Mario monsters, but... geometric shape people or something. This was a huge letdown for me. The character designs in that game are tolerable at best, and either bland or downright hideous at worst. The art direction in general seems off... even uninspired and lazy at points. The locations are... meh, the things you do at those locations are... meher. I guess the underworld place was kinda cool, but then you're only there for like half the chapter.
The plot... well, it was pretty much Romeo and Juliet with Mario characters... though the Mario characters aspect is debatable since they were just geometric shape people again. Would have liked if they were koopas, or yoshies, or thwomps or whatever instead. Or if you want them to have an otherworldly feel to them, they could have been SMB2 creatures.
The game gets some mercy points for making Bowser playable though.