Many saw this as an inevitability after her husband CM Punk (Phil Brooks) left last year. While it hasn't been confirmed that his leaving WWE is the reason for her departure, it can be assumed that it's one of the many factors. Not having your significant other on the road with you anymore would be difficult enough, but considering how Punk and WWE are on bad terms, that must weigh on her even more.
On top of this, AJ Lee had essentially done everything that she could have done in WWE. She's a multi-time champion, former GM, feuded with everyone noteworthy except for the NXT crew, and has been part of the company for many years. She may just be looking to settle down, have a family and move on to a different stage in her life.
One way or another, hopefully we'll see her back in the ring at some point in the future.