Just watched this the other day, and I have to say I rather enjoyed it. The lens flares aren't too bad either - having watched J.J Abrams movies before, I expected them, and you stop noticing after a while so really they just subtly set the tone in the background. Well, foreground, but you get the point.
If you look at the movie as having two narrative tracks (the kid and his father), then the father's story is comparatively weak and unsatisfying. If, however, you look at the kid's story as the main one and his father's story as a complementing narrative, then it works well enough. I guess you could say it's just a matter of perspective.
What I really liked, though, is how it exclusively follows the children for the better part of the movie. In "Act 2" as Bob would say (or is it Act 3? I can never understand his implicit compartmentalisations), when the whole town turns into a war zone of sorts with tanks rolling everywhere, I found myself appreciating how the camera stuck to what the children where doing instead of trying to show what was going on on the larger scale. Much like E.T. did, I guess. But it separates the film from other 'alien invasion movies' like Battle LA or Transformers (not that those movies have much in common anyway).
And those kids can act, I'll give them that.
So any rushing over seemingly crucial plot details like "What the hell are those cube thingies?" can be attributed to the fact that it was mostly irrelevant to the children. The only reason we get some of that is because Joe picks such a cube to keep, and because that scientist who supposedly "understood" the alien was their school teacher.
One final note - the whole military cover-up which Bob claims was a big letdown - I don't see how that's a problem. Sure, anyone could have guessed that the whole dodgy military operation was covering up the alien's existence. It's not an original concept, and it doesn't need to be. In this day and age it is nigh impossible to create something entirely original - that's a fact of life. What matters is how it's presented and how compellingly the story is told.
In this regard, Super 8 is an excellent movie.