Paper Mario: Sticker Star (which I despise) has good music and visuals (Even though I'm not a fan of the enemy redesigns, the presentation itself is really nice-looking and nice-sounding)
Super Paper Mario (my favorite game) has some really bad design in chapters 2-3 and 5-1, both involve codes. There's some other places that could benefit a lot from quality of life stuff like shortcuts, especially in the vertical stages (7-3 comes to mind). The fetch quests in 7-2 that just make you redo the exact same sections again with no variation (other than being easier with Bowser) are unnecessary. I'd have liked Pixls to say more throughout the story and be more than just tools after you get them. Also, from a hacking/modding standpoint (i know I can't hold this against the game but whatever) I hate how many pre-Luigi cutscenes will crash if you have Luigi out. Really limits the neat things you can do with having him early.
Paper Mario: TTYD (another of my favorites) has several sections that are not fun at all, namely finding General White and scrolling through 100 text boxes of "I love you." While many of the ending scenes are adorable (like The Great Gonzales Jr.) some are just excuses to say everyone's happy, such as how we're just meant to assume Beldam is nice to Vivian now despite how she was not only never shown to have a change of heart, but was the mastermind behind the whole conflict and a devoted servant of the Shadow Queen, her just magically turning good as soon as her queen is defeated seems like an asspull. And Vivian belongs with Mario, maybe she can still hang out with Marilyn (who I don't think is evil, just too stupid to know right from wrong) but I don't trust Beldam around her. TEC being still alive is also an asspull though I'm glad he got restored... somehow. Luvbi in SPM is a similar case btw. Grodus makes no sense as they try to explain how this worked with his body exploding but then ignore how his head did the same right after. But I give this one a pass because they do this with Bowser all the time and most RPG villains don't get this luxury.