First off, this is
totally normal. My first 2 weeks of owning an Axe-FX II in 2014 had me regretting my investment, until I took the time to understand the different dynamics a lot of people here have mentioned (FRFR, Headphone, Fletcher-Munson, etc.).
For the broader group of better problem solvers than me:
View attachment 97333
View attachment 97334
Couple notes:
1. You do not need to route your signal chain like that. You can have all you AMP + CAB + VERB + FILTER + LOOPER + GEQ and outputs in the same line. The Send and Return function on the FM3 is sometimes used for more complex routing, but I digress (to each their own)
2. Yes, the amp config sounds flat. This could be from the cab combo with that amp. Check out the Axe Wiki for recommended cab combos and detail on amps
(Friedman C45 Link)
3. Output 1 and Output 2, why is this routed this way? Explain what those go to for a better understanding and why you feel you need to EQ the output going to your headphones?
4. Try a new output routing. Do you have a Scarlett 2i2 or other USB to PC/Mac audio interface? You can use the headphone jack in that device to hear what it is going to sound like recorded, then use the interfaces outputs to route to your studio monitors.
Another recommendation is to go to a factory preset and use the Preset > Save to New Preset number feature. Save a preset you like from the factory to a <BLANK> end of the preset list number and start tweaking This gives you a baseline of how
that model sounds for how Fractal tunes them to their ears. It's a way to re-baseline what you could be missing.
Just some thoughts to get you started.