As far as games go, I think Suikoden 2 is the best. But in regards to actual plot or story, I think Suikoden 3 is by FAR and away the best. Suikoden 3 has all the war-related elements of the 1st two, except with the final "aha" moment of where the story is going. Not to mention that Luc, Yuber, and a Silverberg being the main villains was a fantastic way to go, but also featuring former characters as Easter Eggs.
To me, the future of Suikoden was Harmonia and Hikusaak. Anything not going in that direction IMO is anticlimactic, because the stage has finally been set for where the undoing of the universe will come into play.
Plus, Suikoden 3 featured just SO many gosh-darned Runes, and for the first time really delved into the psychological aspect of owning a True Rune. It delved into Geddoe's sadness over it, Hugo's adaptation to inheriting the pain of the memories, etc that hadn't been touched upon in Suikoden 1 or 2.