Yeah that was disappointing too - although it felt like in a way, I'm kinda glad they didn't do it. Because really, Civil War should have come before Secret Invasion, I mean part of SI is that with the Civil War, they were able to slot themselves in far more easily and it was a way to get rid of other threats.
But... I wouldn't mind a more "adult animation" series that STARTED with Civil War or even just after New Avengers sort of leading up to it. Introduce a proper Luke Cage and Jessica Jones, maybe actually start with New Avengers first couple of storylines - just compressed - for the first "disc" and then maybe for the second "disc" do like the road to civil war, then in the third "disc" do the actual civil war - maybe even as a two parter - and then at the end Cap dies. Disc four sort of is the aftermath and the start of Secret Invasion, Disc Five is the actual Secret Invasion which leads into a sort of "Dark Reign".
Hell I'd be happy if they essentially did motion comics but I would rather see an animated movie - with some care taken. Plus it's been far long enough that no one will bitch about "spoilers" - since honestly, that least Season of EMH was practically like current comics - or like the previous year's stuff. At least some of it.