For me the biggest limitations have been:
1. Runs out of CPU sooner than an FM9, but it’s never stopped me from getting tones I want - it just usually means rejigging some presets or removing unused blocks. I suspect if I were using an FM9 the same thing would happen - ie, I’ll max out whatever is available, just like I’ve rarely had a pedalboard that had free space on it

- but it would ultimately have more flexibility in this regard.
2. I have an FC6 so I have just as many switches and even more controller inputs (external switches and expression pedals) than an FM9, but I have slightly fewer audio I/O, which is relevant if you’re running external pedals or other devices or if, like me, you’re running multiple instruments into it at the same time (I’ve run mandolin, lap steel, pedal steel, banjo, theremin, and even saxes through my Fractal rig at gigs, as it can then handle all the switching thus reducing the number of external devices needed …).
The other differences I haven’t found relevant to me. For example, I never had the urge to run amps in parallel for live shows so I don’t miss not being able to run 2 amp blocks in a preset.
The biggest advantage is that I can fit my FM3 in not only the recently reduced (for some airlines) carry-on baggage sizes but could even bring it as a ‘personal item’, which could halve the flight cost (as opposed to having to pay for a carry-on or checked luggage for an FM9). And for things like musical theatre or other gigs where stage/pit space can be a huge issue for some shows, it’s great to have the very small FM3.