I actually prefer the first Paper Mario as opposed to The Thousand Year Door, but the second one definately upped the challenge level, but pretty much all of the Mario RPG's have been using the same plot over and over again but altering it slightly. The plotline in Thousand Year Door is deeper, but it's not much different from Super Mario RPG and the first Paper Mario.
Are you referring to the whole "collect the 6/7/8 star/hearts and then go to the final area to fight the big bad boss" thing? They've been using that one to death, yes, but I don't think you can really call "Bowser stole the Star Rod, trapped the Star Spirits and Peach, now rescue them" and "A
demon was sealed thousands of years ago that can only be opened by the Crystal Stars, a secret organization plans to
unleash the demon, so they stole Peach to use her as a vessel, so collect the Stars and save Peach" the same plot. Gameplay-wise, yeah, it's similar, but at the core, taking every aspect of the story into account, they're almost entirely different plots. They're at least more varied than "Eggman has this new monster thing and uses the Chaos Emeralds to power it up but then it goes crazy and Sonic goes Super to defeat it". Mario and Luigi: SS did a good job by not being about collecting things, except for the Beanstar Hunt which didn't really take up a significant part of the game.
Just a question, but in your opinion, what makes the original PM better than TTYD? I'm not trying to degrade your opinion, but f you ask me, TTYD improved upon almost every aspect of the original: new, crisper graphics style, original and more epic plot, new major villain, slightly more mature content, etc. I finished PM1 and I'm currently playing TTYD again, and it's as amazing an experience as ever.