I have both the FM3+FC6 and the FM9.
It kind of depends on what you value most, a flexible and easily portable unit that, while it doesn't have as much CPU, definitely has what it needs, and allows you to resize its footprint on a stage or in your luggage, versus the added CPU and the all-in-one design.
While the FM9 allows higher resolution for the reverbs and such, on stage you'll have a really hard time noticing that difference.
Physically, the FM3+FC6 takes up a lot less room and is easier to carry if you use something like the Studio Slips FM3+FC6 bag because they're stacked vertically, making it a lot easier to maneuver through crowds and hallways. I have their bag for the FM9, and, while it fits perfectly, the additional length of the FM9 makes it a bit unwieldy when moving, especially when moving quickly. I am afraid to look for the places I've hit the walls and doors moving my FM9 through the house when returning from playing, but I've definitely heard the collisions.
There's always tradeoffs, and they're both excellent systems to use. Tell us more about your needs, the situations you play in, and whether you're traveling or at home, and whether you need more flexibility for stage placement or in your presets.