I prefer Bowser's Inside Story and Superstar Saga over Partners in Time. Bowser's Inside Story is the best installment for me though. I liked Partners in Time too, but the babies felt clunky in combat by having to juggle A/X for the Marios and B/Y for the Luigis. The baby humor often fell flat, and the Shroobs yelling random gibberish got old after a while. I preferred the Bros Moves coming from a point bar instead of items (not that I often ran out of items, I think). I do like the game's OST and how it often has a darker atmosphere though. But then you have the REAL final boss being one big dodge/block session which didn't need to exist at all.
When I look at Dream Team, it was fine for what it was (aside from the gimmicky as hell Giant Luigi boss battle controls I easily screwed up in). But Bowser's Inside Story did everything it tried better? Story? Better. Locales? Better. Characters? Better. Music? Better. Humor? Better. 2D gameplay in another plane with screen switching? MUCH better. Dream Team was very stop and go with traveling to the dream world to save every random Pi'llo person you come across, and the aesthetic dream world itself was so bland. Using the top screen for Bowser with X and Y buttons and the lower screen for the Mario Bros with A and B buttons was so damn perfect. You could switch between their perspectives at any time with one button press, which made the story always feel like it was progressing with quirky bodily environments explored in the game. The Giant Bowser bosses were gimmicky, but much more tolerable than the Giant Luigi controls in Dream Team. As well as funny. And Fawful as the main villain was positively glorious.
Paper Jam was bland and two-thirds of your experience is made up of playing mini games to rescue Toads. No, really, that is not an exaggeration in the slightest. Story's meh, it is literally just save the princess whereas Dream Team at least tried having a unique villain alongside Bowser. Humor's alright. The areas are all based on generic NSMB tropes. The gimmick of both game casts meeting withers away after thirty seconds when you realize they only use the main Mario cast, in which everybody's personality is the same except for the two Luigis (but that of course means the Luigis never meet even once in the game. Because seeing a talking Luigi made of paper would be weird, I guess?). The Papercraft battles are tedious and boring, I don't know why the exist other than as a substitute for giant Bowser/Luigi battles. But the battle system is probably the best it ever was. Paper Mario only uses the Y button and has his own different moveset, which blends with Mario and Luigi much better than the Baby Mario Bros. did by hogging the hammers and needing to press two buttons for every normal attack.
All in all, if you haven't played Bowser's Inside Story yet, fucking buy it. It can easily rank as the best Mario RPG, even when paired alongside the Paper games (though it rivals Thousand Year Door for me).