Hell, I bought the collectors edition, so I got the day-one DLC included as it was. Really, Javik is not as important a story element as people think: He does not add very much in the way of key plot details, simply another character and all that entails: Another option for your squad, another skillset, two more bonus powers, and extra backstory. The only things the day-one DLC add beyond that, is an extra gun and some lore.
If you aren't a hardcore ME fan, and likely never will be, you won't miss a thing. If you are, your mind was pretty much made up the moment you heard about it.
As for the ending, yes, the ending is horrible. Its broken, and makes no sense unless you come up with some kind of elaborate conspiracy theory, The Indoctrination Theory, to make it make sense. Which, it does. But, lets face it, while Bioware thought about that as being part of the ending, it wasn't. The pieces are just there by funny happenstance. Still a nice happenstance, though.
But, neither killed the game for me. I played it through several times, had a blast with the Multiplayer, despite the unlock system, and the only reason I'm not playing it now, is that A: My friends aren't playing it, and Multiplayer is always better with friends, B: I'm in the mood for a different game, namely Fallout: New Vegas, and C: I've pretty much burnt out on it, for the time being.
Its a pretty damn good game. Even great. But perfect? Far from it. Would've undoubtedly been able to get much closer, but I personally lay that on Casey Hudsons head, the bastard.