Thousand-Year Door is often heralded as the gold standard of what a Paper Mario game should be. A masterpiece. And there are certainly points where I can see why. From the get-go, it's clear that you're in for a much grander adventure than what Paper Mario 64 had in store. The story's a lot more interesting and dramatic, with a few twists here and there, and the main villain has a cold and calculating edge to him that you don't see often in Mario games. The stakes are high, but that doesn't stop the game from throwing in jokes for more lighthearted moments. The chapter structure is toyed with a lot more, whether that be through participation in a fighting tournament or a three day long train ride, so there's a bit more variety throughout. Partners are typically given a lot more depth this time around, with two particularly standout examples a little later in the game (who could hate Vivian and Bobbery?).
Of course, the biggest improvement here is the combat. Partners are really given the spotlight this time around, with their own health totals, and the ability for them to swap positions with Mario to change attack order also doubles as a way to switch who'll likely see the brunt of attacks. Plus, the addition of the Superguard, which is just difficult enough to pull off, introduces more interest to enemy attacks and a bit of a risk vs. reward element that rewards familiarity with the game. These changes come with a plethora of new attacks, items, and badges to create a system with so many more strategic possibilities (and as before, smaller and consistent damage numbers compared to other RPGs make strategizing turns in advance easier). The game maintains a more satisfying sense of difficulty than its predecessor, and overall feels more balanced (though I'm sure there's still a few strategies out there that can really crack things open).
The Trouble Center adds more dedicated side quests, and a slew of new overworld abilities make exploration more interesting. Thousand-Year Door builds on the foundation set by Paper Mario 64 in every single way.
But there's one fatal flaw that keeps TTYD from achieving its full potential in my mind: backtracking. There are so many instances of having to run from point A to point B, only to go straight back from point B to point A. Anybody who's played the game will undoubtedly know what I'm talking about as soon as I mention Chapter 4 (the “end of chapter” fakeout and Vivian being awesome might keep the chapter memorable, but I'm still not sure if it outweighs the horrible design of the chapter or not... you literally run back and forth along a linear path three times), but it's an issue that infuses almost every chapter of the game. And don't even get me started on all the running around you have to do before kicking off Chapter 7. It doesn't help that TTYD suffers from certain hallway-like area design... most rooms in the game will simply see you running in a straight line from left to right, or vice versa. Paper Mario 64 occasionally had the same issue, but you never had to run through each area five times, so it never felt problematic. And I'm just saying... you would never see anything like Dry Dry Desert in Thousand-Year Door.
When I played the game, I completed each of the newly available troubles in between each chapter, and, well... that was very much a poor decision! But I can't imagine that doing them all at the end would feel much better. Interesting troubles are diamonds in the rough, buried underneath much more numerous troubles that just send you mindlessly running around. It's agonizingly boring, and more like an obligation I had to finish rather than anything actually enjoyable. Needless to say, that's not what any part of a game should feel like.
Despite all the advancements TTYD made upon the original Paper Mario, the occasionally mind-numbing progression and loss of a lot of the attention to detail that made PM64 so charming keeps me from calling it a masterpiece or even my favorite in the series... though it's undoubtedly still a great game all in all.