I think that the way it handles the storytelling is absolutely fantastic. I really adore the trinity sight system, especially what you get when you get all 108 characters. I also think the main characters are all pretty awesome - even Hugo. It has a great war battle system, and the battle system, while definitely not as good as the others, was an interesting experiment that is fun to exploit. The skill system is also absolutely wonderful, and it has a great soundtrack.
I understand being disappointed with it coming off of Suikoden 2, but it really is a great game.
I found the trinity sight system to be an extremely poor attempt coming to it shortly after shining force 3. You end up seeing the same scenes over and over with only slight extras, going over the same maps over and over with different parties and you miss out on loads of stuff if you dont do the chapters in the secret order konami wanted.
Still, I'd take suiko 3 a million times over no suikoden