Well, it's interesting you suggest Tir. I mean, he's a nice kid and stuff and he helped you out in S2 as well. But throughout S1 he saw friends and family die. That had to affect him. And then in S2, even though he was doing good things to help out Riou, every one in a while he'd be shown experiencing pain or fatigue with having the Soul Eater. PERHAPS, the soul eater is slowly eating away at Tir. Eventually his soul will be taken and the rune itself will take over Tir's body and do unspeakable things. And then once you beat the Soul Eater host, Odessa, Teo, Ted, Ted's granpa(whoopie), and Tir will come back to life and they'll all do the hampster dance.
Lazlo is also a good possibility. Let's look at the facts. He gets accused of murder by his best friend, bottles it in. Is exiled from Razril, bottles it in. Sees lots of dead people after using his rune, bottles it in. Uses the Rune of Punishment one last time and ends up abandoned in an oar-less row boat in the middle of the ocean, DOESN'T bottle it in. If you take Tactics out of the picture, you can almost see Lazlo losing his mind in the boat shouting "HEY, A**HOLES!!" as he's waving to them. Gets on board the ship, and starts killing everyone in a explosive fit of his bottled up unparalleled rage. He bashes Snows head against the railing until the deck flowed red with his blood and then takes off, building up his power and anger until Suikoden VIII: The Final Chapter.
I don't want to think about Freyjadour being a bad guy. If I had a dog, I would name it Freyjadour. Though I think I did mention an idea that because of some big disaster, he needed to adorn himself with the Sun Rune which could cause him to flip out like his mother did. I think he'd have to if you want to see him at the same age as he was in the game. I don't know if the Dawn and Twilight Runes grant immortality. And even if they did, didn't Freyjadour (I just like saying the name) and Lyon return the runes to their respective shrines?
Riou and Jowy? They could possibly get really upset after Nanami dies of old age or something. Maybe they'd fight again but this time be a little more epic about it. Hmmmm . . .if there's a Rune of Beginning, is there a Rune of Ending?
Anyway, I don't think they'd make the final bad guy someone we were supposed to like. We were supposed to like all the main protagonists. I think we were meant to find Luc to be kind of a jerk when S2 came around. Could he have looked any more annoyed with you in his profile picture? So if you really want to figure out who it could be, look at all the games and find all the ones that were kind of jerks or looked like they might have some kind of ultimatum that didn't involve your army. Maybe it will be Chamberlain Jess. What a dweeb!
"Black Rune, pink balloon! This guy killed Gremio!!!"