In my honest opinion, with Mario RPG, Paper Mario, and Paper Mario 2, you can't go wrong. I don't really feel the need to declare one decisively better than the other, and one doesn't really stand out as that much better than the next. I'd put MRPG, PM, and PM2 in the same class, Mario & Luigi Superstar Saga, behind them a bit, and SPM well behind them.
Mario & Luigi Superstar Saga is a lot of fun. Like someone said earlier, it is a hilarious game indeed and the Bros attacks are great. Still, as good as it was, there was more wandering around(exploring, I suppose) in Superstar Saga than in the others. PM and PM2 are somewhat straightforward in what to do next. As I recall, Mario RPG had more wandering around than PM and PM2, but nothing confusing or tedious.
Super Paper Mario is a fine game, but easily my least favorite of the role playing and "main" Mario games. The platforming is rather simple and not at all challenging. The "rpg" aspects is just accumulating points to advance your HP(maybe some other things I don't recall). The 2D/3D gameplay mechanics work great and leads to some really cool moments. On the downside, you might find yourself constantly switching between 2D and 3D to keep from missing anything. The best two things SPM has going for it are the graphics and humour. The game can be a bit chatty and long-winded, but there is one infamous scene in the game that had me laughing harder than any game ever has.