Personally, I did not like that you have to open the Reflex Rail and manipulate two dip switches to adjust electronic settings. The grips and feel of the marker are very nice, though - and if efficiency isn't a big deal it's a great choice. I thought the Axe had a much better trigger but it was heavier and the marker foregrip can be awkward for some (myself included). Not every one seems to do it, but at least two people I know always have their marker fire a shot out of the barrel just by engaging their ASA on with the AXE.
Efficiency is a deal killer for me, and I'd definitely have to take the Axe if it was my choice between the two. The other thing I like about the Axe that can't really be quantified is the number of modifications you can do to it. This includes new trigger frames, polishing the poppet(/new poppet tomorrow?), lighter bolt, new dynamic bolt, grip extender, and maybe others I haven't thought of (plus the same you can do to the Reflex Rail: underbore barrels and new board). These changes can give the marker a softer shot, quieter shot, more comfortable feel in the hands, and make it much more efficient. The Reflex Rail is not quite so dynamic in its ability to transform to a better marker with small investment, and a tuned/upgraded Axe is in my opinion in a higher tier than the Reflex Rail.
(edit: You'd think I could distinguish between qualified and quantified.)