The autofocus has never really bothered or hindered me across the X-E1/X-M1/X-Pro1 range, it just requires a different mindset to a DSLR. In terms of my hit rate the accuracy of my Fuji bodies are miles ahead of any DSLR I've used, I took 3000 photos with my X-E1 in the US last summer, not a single out of focus shot, not having to worry about micro adjust etc is bliss.
I've not used the X-E2 yet, but the CDAF only bodies have done everything I've asked for them (
http://www.flickr.com/photos/harry_s/sets/72157634005095926/), so I'm looking forward to getting hold of a dual AF body, but I'm in no rush.
I also don't think the range is that confusing, especially compared to Sony who have what is essentially 3 systems with interchangeable names, confused more by NEX adopting the Alpha name (which is also a mount, but not for what was NEX!), what's more, Fuji are more than happy to continue supporting models long after release. I'm more than happy holding on to my x-Pro1, it may be (or have been) superseded but Fuji have been pretty insistent that they will continue to support it as their flagship.