So uh...

[Koopaul]

The Paper Mario series was never very deep and there was never much of an idea of a threat. The characters are all very flat and there only to serve the purpose of getting Mario closer to the last boss.
In Mario RPG we are derailed, given subplots, and we grow to care about the characters.

Not really, maybe somewhat with the first Paper Mario but certainly not the second.

I know Super Paper Mario is not an RPG, but as far as plot and characters go, it is king in Mario games. Have you ever played that game? It dwarfs other Mario stories.

Even Rawk Hawk was more interesting than characters like Koops or Yoshi Kid.

Koops? A flat character? Not at all. Like Mallow he had a motive to find out what happened to his father and learn to be more brave. You obviously don't remember the game very well.

The M&L series definitely has personality, but lacks plot.

Lacks plot? M&L has a much more interesting plot than RPG... No offence. The plot changes half way revealing a that your mission to save Peach's voice was a false one, then when you think the main villain is defeated once and for all, she transforms into something new... Now a new mission is underway to find the Beanstar... All that! RPG just had the simple plot, collect the Stars, defeat Smithy.

Another small thing that annoyed me is that the PM series never gives you a very fleshed-out battle system.
It's all Mario-centric while SMRPG had all five characters on equal footing. Regulating the battle system to just one character seems lazy and takes away from my experience with both PM games.

The battle style? That's the one thing I loved way more than RPG. It was a unique and simple way of fighting that expanded on the timed button pressing of RPG. It certainly a style Mario could call his own. The whole "hammer can't hit flying" and "jumping on spikes hurt you" added the physics and style of classic Mario games that RPG didn't have.