It's telling that whenever you talk about PM64 and Thousand Year Door you have people reminiscing the entirety of PM64 versus people remembering moments in thousand year door that were really good but the player had to go through something annoying through backtracking or badly paced segments the first time they played
Twilight Town and the stupid General White globetrotting quest were so bad in backtracking and padding things out, but those two have some really cool moments like Doopliss switching bodies and using the cannon to reach the moon (and get to the moonbase to hear that
amazing theme)
Paper Mario 64 you can just throw any chapter and people will be like "Aw yeah that chapter was fuckin great" except for MAYBE the Toybox/Flower Fields chapters but those had fetchquests that didn't really waste that much time and told you right away what to do and where to do it since the N64 was being pushed to its limits already
I can relate to Flower Fields being boring. I never really thought about it, but upon replays, I lose a lot of motivation right at Flower Fields. The constant back-and-forth in that chapter grinds all momentum to a halt. But at least the character interactions are fun, and the boss makes up for it, too. I can
see how people can say the same about the Toybox, but it's so undeniably charming that you tend to gloss over the minute backtracking that chapter has.
Thousand Year Door is almost insulting, like the pirate cove where people asking you to return to the same areas three times on a complete whim with no plot importance nor payoff before anything happens. At least in Flower Fields, you feel like you're accomplishing something by helping the denizens. The pirate cove intentionally wastes your time with fetch quests that amount to you effectively ending up back where you started in terms of plot progression.
The best comparison of the two is the sewers for both. Think about 64's fast travel system. From the town, you go through maybe two screens, enter the sewers, then head left for the starting areas and farther left for the late game areas, and I don't even think you encounter a single enemy on the way. In Thousand Year Door, which had the exact same fast travel system, you still need to navigate the entire level up to that point, solve the same puzzles you solved to even unlock the fast travel to begin with, stumble around a few times because it's nearly impossible to memorize what takes you where even on a return playthrough, and then navigate the whole area in reverse just to leave.
Don't get me wrong, Thousand Year Door's highs are greater than any moment in 64, but its lows are both greater and more plentiful than even the worst 64 suffers from. I genuinely would recommend anybody playing Thousand Year Door for the first time to just use emulator speed hacks or cheats to speed up traveling, because it actively detracts from the experience.