As I understand it Christian Gossett (who directed Prelude) was supposed to direct Axanar as well but left the project in May 2015.
Here's the post in the production blog: http://www.axanarproductions.com/captains-log-may-12-2015/
There's some chat about it in August on this TrekBBS thread: Star Trek: Axanar
I didn't read more than a handful of posts, but from what I see I can see that:
1) the were certainly "differences" beyond creative concerns that lead to his departure, whatever they might be, and all sides had their own spin.
2) the Axanar team had no idea what they were doing as late as August. A lot of talk on how they'd be fulfilling KS pledges without a completed film. Keep in mind at the time of the posts the July, 2015 fulfillment date had passed, and they were still not close to even beginning pre-production on the actual movie.
I am also forced to wonder how much of Christian's departure was due to their "visionary creator's" behavior, as Tony Todd likewise implied.