Come to think of it, Gil is probably a member of the Logos but he is worsening the war so that he can make more money from the conflict and so that he can possibly kill off some of the other Logos so that he becomes more powerful. Think of it that he did intiate production for the 5 original Gundams (of GSD not GS), Zaku Warrior, and I'm assuming he also was strongly behind the production of the Gouf Ignited. He's also behind FAITH and is most likely deeply involved in genetic engineering and cloning, unless somehow Rey is his nephew/son who just shares a lot of similarities to Krueze.
Personally I think what will happen in the story at this point is Archangel will interfer with the upcoming battle, Heine will be severly injured or even killed, Impulse will be trashed, the EA will bring out their new Gundam piloted by Stella. After that new Gundam trashes up some ZAFT stuff Shin will get the Destiny. After that who knows what.
I think that Freedom will be trashed by Shin and rebuilt to be better than ever. I also believe that Athuran and Kira will join up to fight the Logos and Shin will probably join them too along with a few other main characters. What will happen with that is Rey will probably stay with Gil and field a powerful all range attack mobile suit.
Anyways, just my random thoughts thrown up onto a post