I consider Mana Khemia 2's plot to have a soft "Gainax End" last chapter where the build up of the main 2 story paths stops momentum, loose threads are forgotten, the tone reverts to the early-game sillyness and a far bigger threat is introduced (the true final boss) but is subsequently treated like a joke because of the tone shift. The game was always eccentric in tone, but it definitely felt all over the place at the end. Either way, it's still my favourite game of all time.
Terranigma is a masterpiece but the Starstones fetch quests halts the momentum too much for my tastes. It's the one reason why I hesitate to replay it.
Suikoden II is a story that can change dramatically depending on the things you do, but they're quite arbritrary and you're also not really told what those things are. It also lacks immediate feedback if you did change the story in some key places. It's one of the best RPG's ever, but you need a guide to get anything other than the standard ending, otherwise I can imagine the pacing getting destroyed.