Maybe Paper Mario 1 and 2 are the most well made installments. But they just didn't feel very special when I'd already seen it all done before and done better in Mario & Luigi. Partners are overrated, the item restrictions are ridiculous, and PM2 in particular suffers from poor level design and bad audience mechanics. It's all basically Mario & Luigi but more heavily flawed. Between the two I do prefer PM2 nonetheless, but to call it my favorite wouldn't be right. That just isn't the direction I want Paper Mario to go in.
Then there's SPM. I cannot begin to describe how overrated that game is. It's the pinnacle of fanservice, going over-the-top with original characters and story, while neglecting to have actually good gameplay. I moderately enjoyed this game the first time through, but the moment I went back to PM2 I just thought "man, this is so much better than SPM". SPM had good points but the negatives far outweigh the positives. It's my least favorite Paper Mario for sure; Paper Mario needed something different and I appreciate this game for trying, but it simply didn't work out.
Then Sticker Star came around in 2012, and became even more controversial than SPM. The most hated change by far was the removal of story elements and original characters (save for Kersti and some bosses), and that alone is 80% of this game's criticism. And I'm going to be blunt. I don't care about that stuff. I never have. That's not why I got into Mario RPGs in the first place. All that matters to me is the gameplay. ...And Sticker Star maybe didn't excel there either, as it still had some major flaws, but to me, it was a lot of fun. More fun than I'd had in any earlier installment. It succeeded where SPM failed, and the sequel, Color Splash, managed to improve on it even more. The sticker limits were lightened so that every card was the same size for a limit of 99, paint added an extra level of strategy, and it just overall improved on a game that I feel was already great. As controversial as this may be, this is my preferred series direction and I want to see what more can be done with it. Add original characters and story if you want, won't make a difference to me. It's the only time the series ever stepped out of the shadow of Mario & Luigi.
So overall, I'd rank them CS > SS > TTYD > 64 > SPM. I don't care what people say about the newer Paper Marios, I will defend them to the death.