AJ has never appeared in every episode during a season - despite being a series reg since the beginning of season 4 (I believe it was) - but if memory serves me correctly, he did have an increased presence in seasons 4 and 5. It's possible that they lessened his appearances a bit this year - I don't know how many episodes he's missed off the top of my head, so I can't compare it to previous seasons.
I get what you mean about rotating everybody, but those three (AJ, Bob and Anna) are arguably the three most minor of the cast - Anna and Hill are the most minor of the CSIs, but Anna's role was already somewhat lessened before this season started, so it makes sense that she'd be the one to end up in fewer episodes out of the two of them. (She said in an interview a while ago that she was on a 'part time-ish schedule', presumably because of her family.)
Plus, AJ does stuff besides NY, so having fewer episodes gives him a chance to go do that stuff (like the Ghostfacers web series that's coming up, and I guess he filmed his role in the independent film Skateland while working last season).
It sucks because I love Adam, and I personally think he adds something when he's there (and that something's missing when he's gone), but I'm used to it. *shrug*