I actually really like suikoden 3 because it manages to do so many things not just different from other suikoden games, but different from any other rpg I've ever played, and it does a lot of them well.
The stat system was really good. I loved having a weapon skill stat that made you do counter attacks and parries, so you could be a really skillfull fighter rather than just a really muscular one. (I know all suikoden games have this stat, but it made a bigger difference in 3 due to the counterattacks and the fact that you actually moved around during combat and could get surrounded.) Also, armor was incredibly powerful, which made certain parts of the game really easy (like when you're a knight leading a party of knights) but because you're constantly switching parties from knights to nomads to civillians, it really made being a knight in full armor feel different from anything else -- like you could walk around and dominate the battlefield. I thought that was interesting.
The plot and characters were really amazing when I first played it, though it was my first Suikoden (I then went back and played 1 and 2.) The underlying progression of the Suikoden games also doesn't change very much between games. The best games in the series are all pretty similar in that way. Suikoden 3, even if the story isn't as emotional or wide in scope as 2 or 5, does a good job of making the formula feel really different up until the final part of the game, when everything comes together. That was pretty cool. Also, you get to ride a griffon.