I do must admit, Chapter 4 of TTYD took Doopliss' trolling too far. That chapter would take about half an hour if not for all the copious walking it makes you do (which I always felt like was why they left the backtracking in)I think some parts aged badly or are just overlooked like the horrible backtracking in gc version.
But aside from that, I can't think of any part of TTYD I'd call poor game design
EDIT: Super Paper Mario had the best story in the series, hands down