I did have a better time with Super Paper Mario because I barely ever seen nor personally played TTYD. PM64 is also great, but platforming with rpg elements does make a respected combo.
Honestly, gameplay aside (though Super's platforming focus is way more fun, IMO, and much easier to dodge attacks), Super just has the unequivocally superior story - its narrative, of Count Bleck wanting to destroy all words, is ever-present throughout, unlike Grodus' vague plan.
Count Bleck's actions also directly impact the various worlds, by having his black hole grow larger as the game progresses, not to mention what happens to Sammer's Kingdom, and his motives are actually explained - it makes sense why he feels this is the best plan. NONE of this is true for Grodus.
Paper Mario 64 has a better story than TTYD - because Bowser's an actual threat, straight-up defeating Mario at the start and providing a clear enemy throughout. Grodus is a non-factor for most of the game, and the Shadow Queen comes out of nowhere at the very end - they're bad villains.
..."Fun gameplay" is subjective, and depends on the person's interests - and in this case, I had a lot more fun playing Super Paper Mario than 64 or TTYD. Those two games were made for CRTs, and thus timing action commands is made trickier on flatscreens; there's also the boring Peach segments to consider, and the backtracking to find General White.
In my case, I tried to replay TTYD via Dolphin last year, yet I couldn't bring myself to finish that true slogfest - the gameplay bored me, the story bored me, none of the characters were interesting, and I really hate the Peach segments and the restrictive level-up system. I did play a good chunk, but quit at that stupid General White part.
That last point? I fully agree with you there; the last new Mario RPG was 2020's Origami King, which...meh, bored me even more than TTYD did. It's a real shame that the M&L team went bankrupt after Bowser's Inside Story 3D, because that was a damn-fine remake; though Paper Jam was also mediocre as hell...I did enjoy Dream Team, though.