Very true. Technically Batman Begins is a sequel, but I see it separately from the previous films. In regards to Abram's film, I would argue that it is its own film, especially considering the talk of there being sequels (with the same cast) if it's successful.
I'm not sure how Batman Begins qualifies as a sequel. Yes, there were previous movies with the same character, but those were clearly part of a different continuity. Does Tim Burton's Planet of the Apes count as a sequel?