ME3: Conclusion

Indoctrination theory can be discounted, Bioware has let it be known that they have no intention of changing the ending of the game, but sometime this summer will release free clarification DLC that 'should' clear up the plot holes and major problems, even though they tried to sell it as a favor to the fans who "Need more time to say goodbye to their stories."

Aside from a complete re-write of the ending this is pretty much as much as anyone could have hoped for, so I'm at least happy that they took this issue somewhat seriously, though I wish it wasn't done in such a patronizing way.

Bioware, you didn't need to do this, so I appreciate it. Don't think you're off the hook yet though.