The story gets way too convoluted in the end, it's like they're trying to cram an entire separate game's worth of plot into the game at the end. Too many names to remember that you can't attach a face to initially. So it's easy to forget who's who.
Suikoden games have 108 characters, and I've never had that problem with Suikoden. So it must be TRS' problem.
Ultimately, I prefer Berwick Saga. Better, easier to understand story, more well-developed characters. And the character balance is just amazing. There's only one useless character, but he's meant to be a joke. Berwick Saga is harder, but it's more balanced at the same time, and you don't have to think "hmm, maybe I should have spent more time arena abusing," since that doesn't exist in BS. There's a proper strategy around everything in BS, no time-consuming power leveling involved.
So I eventually gave up TRS at Ch. 37, the story lost my interest.