I think the series should have a definitive ending. Final Fantasy is a series of only nominally related stories and can therefore continue into infinity with no issues. As a self-contained and interrelated series of stories, Suikoden needs to have an ending. If you look at the series as one continuous story, it needs to be structured and have a beginning, middle, and end. Otherwise the series just limps along like a horror movie franchise with 15 sequels that just doesn't seem to be trying anymore. I don't want to see that happen to this series. Leaving like it is, with no clear resolution and lots left to be discovered, is better than that.
As for SVI, it could be epic and could serve as both beginning and end to the series. Set it in the Nameless Lands after Suikoden 3. The Nameless Lands were first mentioned in S2 and we have never seen any details on them. All we know is that Thomas and Hallec come from there and that they have more than 100 species of venomous spiders. Have the Nameless Lands and Kamaro united in a battle against Harmonia. Hikusaak is the antagonist, but we find out why Harmonia is collecting the Runes and its not for as sinister a reason as everyone thinks. I don't think its some personal crusade for Hikusaak to gain godly powers or anything, Suikoden has never been that simple. Except for Graham Cray, Suiko antagonists tend to have multifacted motivations for what they do and think they are doing the right thing (Jowy, Luc, Sialeeds). Maybe Hikusaak is trying to collect the Runes and keep them from doing to people what they did to Luc? He nearly destroyed half the world, don't forget. Maybe Hikusaak wants to seal them off and free mankind from the Runes' bondage as well. If his goal is important enough, he would have to do morally gray things to acquire the Runes (Gate Clan Massacre) because its for the Greater Good. I wouldn't want him to be a cardboard villain ("I wantz teh Troo Roonz for all teh powerzzzzzzz!!!!!").
As for dangling plotlines: Viki (and little Viki), Jeane, and Yuber/Pesmerga could be easily reconciled. The first two with simple recruitment quests if need be. The third would need to be a longer storyline, but it could be done. We don't need to see every country in the world, but knowing what the remaining True Runes are would be nice. Even if we don't know where they are, what they do, or who has them. Names and appearances would be fine for me. Have a room in the One Temple in Crystal Valley that has 27 statues (like the Sun Rune Statue in Sol Falena). Inspecting the Statues would open a dialogue window that would say the name of the Rune that is intended to be sealed there and its current location and/or bearer (if known ... some could read "unknown"), along with a picture of the Rune. Done.
I would like to see Leknaat temporarily recruitable (as a non Star) and see her finally have it out with Windy (I think that would be a nice way to bookend the series). Have Windy be a Neclord-type boss late in game, but not the final boss and not directly related to the main story. Maybe even having Windy be repentant for what she did and the game giving you the option of taking her half of the Gate Rune (and the Sovereign Rune) and leaving her and Barbarossa to live in peace and obscurity in some small farmhouse in the Nameless Lands together.
In terms of Gameplay I would like your decisions to have more lasting effects on the plot as a whole. Maybe have more than 108 characters and give you choices as to who is what Star. Do it like Chrono Cross where recruiting one person locks out the possibility of recruiting others (maybe even make it impossible to get all 108 if you recruit the wrong people). Also having choices you make having repercussions late in game (people will remember if you acted like a jerk to your sister in the beginning of the game and will be less likely to join you or help you later). I would like to see a Charisma score for the hero that shows how people feel about him. In most games its "I have a True Rune and instantly everyone loves me."
Returning characters? A few, but I don't want to see Suikoden All-Stars. If you're going to give options on who to recruit, you can have a lot of returning people, but I don't want everyone to be there. You could have all the True Rune bearers come back, I guess, but I don't think I'd like that. It sounds kinda like fanfiction to me. I think Tir, Riou/Jowy/Nanami, and Lazlo's stories are over. It might be nice to pop in on Hugo, Chris, and Freyjadour, just to see how they have matured with their Runes. I would like to see Geddoe and Queen having a lot to do with the story.
Heh, just my two cents.