Super 8 had a great first half and then petered out. Star Trek 2 had a weak ending (although most of the film was pretty weak). I thought the very ending of Lost was fine but the larger ending was pretty weak. Didn't see Alias, but heard that one ended poorly. Heard similar things about Alcatraz and Fringe. MI3's ending was forgettable. Etc.
Gone' Fishin had a crap ending. Actually I can't remember anything about that one and it seems funny now that it was written by Abrams.
Abrams is great at set up but seems to struggle with balancing mystery versus reveal as to what's in the "box." Even if you disagree that his endings are weak compared to those of other movies, it seems apparent that he is better at set up than conclusion.
To be fair, good endings are hard to formulate and execute, and most movies have weak or forgettable ones.
Hopefully Disney's requirements re establishing a foundation for subsequent movies doesn't mess with the ending.