I'm not a huge fan of combat all the time myself, but honestly when there's a grand total of two actual factions and they're warring with one another, there's not much room of things that aren't combat. If there were, say, multiple organizations that were all in a cold war with one-another (Multiple organizations that consider themselves to be the [i]true[/i] protectors of the multiverse and don't recognize the authority of the UMMA, SE having to deal with working in universes that are in a secondary faction's sphere of influence, that sort of thing).

Barring the introduction of new factions, the introduction of splinter factions within the groups (I could see an internal schism within the UMMA being an interesting in for lots of down-and-dirty politicking, or SE agents receiving conflicting orders from their higher-ups.) could also provide an interesting plot. If you've ever read Chronicles of Amber, it's a very good example of what I'm talking about: People who all have the same primary goal (Save Amber) and conflicting secondary goals (Become the sole ruler of Amber). If you've ever played VtM, the Camarilla are another good example of an organization staffed entirely by people who are actively working against their peers at all times.

Of course it would probably also help if Shadow Eternity had some sort of motivation beyond "[i]Grr! We're bad guys who like to kick puppies and do bad guy things![/i]" and the conflict between SE and the UMMA was something more akin to the Zeon/Federation conflict from Gundam but hey what's done is done I guess and if the GM wants it super clear cut I guess that's his choice and there's not a lot we can do about it.