It's difficult to explain but I'm going to try.

Paper Mario games have good and hilarious writing but bad stories.  They're bad at tying events together and bad at developing characters.  Essentially they're Mario games with RPG elements more-so than they are RPGs with Mario.  

For some this is fine.  A Mario game with some RPG elements is all a lot of people ask for.  However, some want more.  For example, some people don't just want a dialog heavy Mario game, some want an actual RPG that tells a coherent story that involves the characters.  Compare the character development of Flurrie of Paper Mario TTYD with the character development of Mallow (SMRPG) with the character development of Almaz von Almandine Adamant (Disgaea 3) and see what you get.  Flurrie gets almost no development and Almaz gets a crapload.  As for Mallow, he's closer to Almaz.  Mallow actually changed a lot over the course of the story going from a crying little puff who didn't know where he came from to a strong companion of Mario who learned where he came from and resolved to continue on his journey with Mario to save the world.  Mallow wasn't just there taking up space, he was part of the story.  Flurrie wasn't really integral to anything really.  She was there for her little area where you get her and then she just got shuttled around with Mario for the rest of the game.  Heck, Flurrie has more in common with Mario's hammer than Mallow in terms of character involvement in the story.

People can hem and haw all day long around the subject but if you shove opinions out the window and examine each game critically, you'll notice that the Paper Mario games had shortcomings you won't find in Super Mario RPG such as the one I just pointed out.