I agree that, aside from cost, form factor is probably the most important consideration. Do you need the versatility and portability of a floor unit?
The second consideration you should make is the kind of sounds you're going for. Are you a meat and potatoes kind of guy (drive, amp, cab, delay, chorus, reverb) or are you closer to somebody like Dweezil Zappa who goes nuts with effects? In a single patch, the FM3 will be able to do pretty much any traditional Amp+Cab rig plus staple effects like delay, reverb, chrous. The Axe-Fx III however can do that plus all kinds of crazy routing and has the CPU to support multiple instances of almost everything. Each patch in the III has the room to let you get pretty nuts. The FM3 will "merely" let you do only one or two nuts things per patch. You'll still be able to do neat tricks with scenes and automation and stuff, but you'll be doing those things under tighter constraints. Personally, I own an Axe-Fx III but I'd be just fine with an FM3. I'm more of a meat and potatoes guy. But, it's nice not really having to really worry about hitting the ceiling when I'm building sounds.
The biggest practical difference summed up, performance wise, is going to be that with the Axe-Fx III, you'll have an easier time making "kitchen sink" patches with everything you could want in them. With the FM3, you'll need to work with a larger number of patches to do the same thing.
