The Kemper and FM3/9/Axe III fx are very different products IMO.
The Kemper is targeted at tube amp + pedal board players that have made the jump to digital. The Fractal offerings (and NQC, and Helix) are really framed more around computer routing and blocks processing.
Two very different approaches, mostly the same result.
If you want to spend most of your time USING your new digital amp, the Kemper is the best product out there. It is VERY easy to get to about any tone you can imagine and to have it sound great.
If you really like messing with your tone in complex ways (combinations of series - parallel - and more setups of blocks), The FM3/9 are going to be better products for you.
Just a note: I don't think the FM3 is a good option for live gigging at all. If you have any hope of doing this successfully, the Kemper Stage is a much much better option. The FM9 is a different story. As stated above, this is a more apt comparison of apples to apples.
Here is my overview comparison (scale 1 = slightly better, 2= more than slightly better, 3=noticeably better):
1) Amp Tone: Kemper (2)
2) Efx: FM9 (1)
3) Routing and flexibility: FM9 (3)
4) Ease of use: Kemper (3)
5) Gigging: Kemper (1)
6) Recording: FM9 (1)
As you can see, it isn't black and white. Personally, I greatly prefer Kemper. I gig and am an old tube amp snob. YMMV.