One 2-p competitive game I could imagine would use all the expansions except Space Marine Pack 1:
- Base Game Blood Angel Marines vs. Tyranid Enemies in Base Game Locations
- Deathwing Expansion Marines vs. Base Game GS Enemies in Mission Pack 1 Locations
Both players would play parallel solo games, taking turns phase-by-phase, and pulling a single event card with its effects on both players. The first one to die would lose, of course. Otherwise, the first one to complete location 4 would win. (Note: First player disadvantage for "losing first" is balanced by an advantage for "winning first")
Then swap missions after (keeping the same location set ups)and make it the best aggregate score? That way you eliminate whining that one player got harder locations than the other.