Based on talking to some of my software developer friends, the cost of WotC developing a new application in-house is so prohibitive that I'm seriously starting to doubt that's what they're up to. There's also such a large installed base of PCGen users that I don't see why WotC would want to eliminate that potential revenue stream.
As one of these friends posited, it's possible that WotC was not happy with CMP's performance, and simply want to either shift the creation of datasets in-house, or to a different licensee. I can honestly see WotC getting into the dataset business. While it's a lot of work, it's nothing compared to actual software development. They could hire one designated dataset guy and probably recoup his annual salary in the space of a month or two.
Basically, owning eTools was not profitable for them back during the d20 boom, ergo, I can't see owning/developing a similar product suddenly being profitable now.