I think the bug tracker itself should be advertised to every game company out there. It works so well with Arcen I'm sure other companies would benefit from it. (I know a few that need something like it).
Anyway, the only issue I can see is the massive reward from capturing a planet on Betrayal mode. What if, during that mode some of the resource stockpile is lost during the invasion? (damaged, destroyed or as a result of scorched-earth tactics by the defenders... maybe difficulty-dependent). Otherwise I think it'll always be an issue... until the hydral get some of their own local/political deals they can't colonise moons but can capture planets with pre-colonised moons full of resources to fund armada construction (with costs balanced against the income without moons).
I'm not sure it's a big problem... just pondering balance. (I feel like Sorcerer King has been eating at my suggestion-time this past week, I'd post more bugs here but I'm struggling to find them. Just enjoying the game instead... which isn't terrible by any measure.)
[edit] Added ticket:
Betrayal mode Balance: Resources captured from enemy worlds
http://www.arcengames.com/mantisbt/view.php?id=16009