I know this is an old thread, but after reading through it, I felt like I needed to comment on it.
I don't think we will see Harmonia taken down in any of the recent games. Though I do expect their involvement in them to increase. I think in the final game though, it will revolve heavily around Harmonia. As we can tell, Harmonia seems to be good at making enemies and seem to be weakened the most at their southern borders. Though I am sure they got something there to protect themselves though. However things will not break out for them from the outside. They will probably begin from the inside. Let's review possible members of Harmonia that could possibly begin to start or become involved in a rebellion.
Sasarai: After the events of the Second Fire Bringer War, he probably has had of personal issues that he has been trying to deal with. This could lead him to question his superiors and might cause him to fall out of favor with them. In that time he then begins to see Hikusaak for what he really is and realizes that Luc was telling him the truth about their origins. Using his power within Harmonia, he begins to secretly feed information, supplies and weapons to a rebellion army that has formed.
Clive: Clive fought in both the Gate Rune War and the Dunan Unification War. His reason of course was to find and kill Elza which he did in the Dunan Unification War. However after the war, when he eventually returned to Harmonia, he might have began to suspect something about that whole Elza situation was not quite right. So he begins looking into it and eventually discovers the truth. He is then left with the choice of ignoring the truth and not trying to do anything about it or confront his superiors. His thoughts then drift back to the Gate Rune War and the Dunan Unification War. He remember seeing people fighting for what they thought was right. He then comes to the decision to confront his superiors. His superiors however apon being confronted, decide that Clive is now a threat and try to have him killed. Clive however manages to barely escape and ended up joining the rebellion army that has recently formed.
Nash: He is definatly a while card in this one. On one hand he works for Harmonia, on the other he is assumed to be married to Sierra. Which I am assuming is so. In which case if she decided to aid the rebellion, chances are he would have to as well. That or feel her wrath. I think what he chooses would be obvious. lol.
Sierra: If she is indeed married to Nash, she might be living in Harmonia at the time. As a the bearer of the Blue Moon Rune, she could possibly have been shown a vision from her Rune of what is to come if Hikusaak. Knowing that she could not stop him alone, she decided to join the rebellion army and forces Nash to join as well.
Geddoe: As we know, he is probably still working for the HSFDF at this point. However due to the events of the Second Fire Bringer War, Hikusaak now knows that Geddoe has the True Lightning Rune. He forms a plan to trap Geddoe and seize his rune using the power of the Circle Rune and capture it, just like Luc did before. However Geddoe, perhaps being shown a vision of what is to come by his rune, comes prepared. A battle occurs and the battle results in a small part of Harmonia being desimated. It also results in the death of Geddoe's entire unit. Both Geddoe and Hikusaak are no where to be found. Later on though, Hikusaak reappears wielding not only his rune, but the True Lightning Rune as well, much as Luc did before in the past. However Geddoe remains missing until the end of the game when he joins up with the rebellion. The effects of the True Lightning Rune on him however begin to fade. Such as he looks a lot older and is beginning to physicly weaken.
Ok those would probably be the only reoccuring stars of destiny. Now on to my idea for the hero.
Hero: Born into Harmonian 3rd Citizenship, She has not led a good life. Yet it was a happy one, until that fateful day when an explosion could be heard all over Harmonia. It was the sound of the battle of the True Lightning Rune vs The Circle Rune. Her home was near the the outer edge of where the devistation ended up occuring. As the explosion occured, the True Wind Rune appears before her and chooses her as it's next bearer. The True Wind Rune then shields her from the explosion. Her family and all her friends though were killed. At the time when she get's the rune she does not know what is going on, nor does she have any real control over it. Now as to how she gets involved in the rebellion, I am still working on that, it is not an easy thing to work in but it does have possibilities.
Now as for the other true rune bearers. It is possible they are alerted to what occurred in Harmonie through their true runes. Leknaat then appears before each of the good ones and informs them of what has happened. Realizing that Harmonia needs to be stopped, they make their way towards Harmonia. While making their seperate ways there, some such as Tir, Riou and Jowy decide to try to gather forces from their respective countries that they helped to establish, in order take on Harmonia.
There are still some wild cards though. First we have unnamed true runes but it is best not to get into that so I will focus on the ones we know.
Beast Rune: Currently it's location is unknown. It is possible this could end up in the hands of a good guy or a bad guy.
Rune of Change: I have a feeling the Sindar, or at least this rune, will make a return in the final game. What side he or she will be on is really hard to say though.
Yuber: While we can guess that he will probably be on Harmonia's side, there is always a chance that he will turn on them.
Windy: Yet another Wild Card. It is possible that she might use this chance to try to steal another true rune for herself. Her and her half of the gate rune are sure to make a return eventually and i think it will be in the final game.
Barbarossa: We can not count him and his Sovereign Rune out either. Though I see his return as a good guy rather then a bad guy. Or perhaps he is still Windy's b*tch. lol
Needless the final suikoden game should be the best. I just hope the series last long enough to make it to that one. In the end though, I see Harmonia getting crushed, once and for all. lol