I've had custom basses from both. While Jon will build you pretty much anything you desire, Alan has a more fixed menu of options - which is in no way a criticism.
Personally I found dealing with Alan a much more pleasurable experience. He got my build 100% correct... And on time... Neither of which I can say about my Shuker. Still an outstanding bass but Alan's work is another level. IMHO, YMMV, etc.