Wow, you share the exact same opinion as me. Chapter 2 in TTYD (the tree) is probably the part I hate the most about replaying the game. Having to blow the Punies is so irritating, and if you drop or miss one, have fun. I can see how Chapter 3 might not be to everyone's liking, but I think it is pretty good despite the large number of battles. I mean, it does introduce Yoshi, after all. Twilight Town is in the middle of enjoyable and not enjoyable. I first time i played it, I didn't read the bird telling me the guy's name, so I had to look up the name. I dislike the mystery forests in both Paper Mario games, so it doesn't help Twilight Town. The train also is pretty bad. It is an interesting concept, but it can take a long time to do if you forget what process, and it is boring, overall.
I also think the Moon overstays its welcome. Despite all of the shortcomings of TTYD, it is still an amazing game. I really like Paper Mario 64, and would probably rate it better than TTYD, but that is mostly due to nostalgia. It would be nice to have a remake or VC release of TTYD.