Okay I have seen people complain about the Broken Steel expansion and I get what people are upset about. It really does invalidate some decisions but that doesn't mean every after release DLC has to do this.
So here is my idea on how they can do it right, even though they won't do it at all.
After the battle of hover damn simple recognise whoever is in control with their military presence. Then simply say a new threat has emerged, Vault 22 residence have returned, Yes man has mutanied or downloaded himself to another council whatever. The threat can be whatever. This works because it
1) Doesn't invalidate any endings
2) Still continues while representing the players choices.
The Faction head (which will probably be you, House lets you handle a lot of day to day, you are the NCR commander in the area, you are Cieser chosen governor and Independent well you are running things anyway.) you have to deal with this new threat which will take you to a new area like Broken Steal without screwing your choices over (I can't stress this enough).
Then you simply go about dealing with this threat.
Now this could be as simple as going to a new area or have these creatures, faction, whatever start effecting different areas of the map which you can help defend, recapture, ect. Or it could be as simple as just a new area.
Something that should be added in my opinion is some new creatures to the wasteland like many people have been asking for.
Anyway just my idea on how they could do an after Main Quest expansion without pissing off half the fan base.