I picked up the collectors edition recently for a pittance, found the protean to be incredibly dull, and rarely brought him along. Dude might have died in the cargo hold for all I knew. Got the Leviathan DLC as well and while I didn't think it was particularly good from a play perspective (in that it wasn't all that different from what was already in the game save for that one bit near the end where you basically play a single player version of one of the multiplayer missions), it did serve the purpose of finally answering some of the lingering questions the ending had for some.
As for the ending, I first saw the non-EC version having forgotten to download it. After that, I saw the EC and found both entirely acceptable. Even without the EC or Leviathan, I didn't feel there were wide enough story gaps nor sufficient evidence to justify the common Indoctrination Theory. Hell, even before I played the game that theory was shaky.
Personally, I won't be getting any more DLC for the game. It served its purpose and in spite of the raging of the internet I found that I quite liked it.