THIS IS THE BIGGEST FAULT WITH THE AXE FX, IT'S TOO PERFECTLY DIGITAL TO PERFECTLY SIMULATE AMPS. Fractal needs to add some chaos algorithms to the AXE III.
If your goal is to fool people on your recordings that they're actually listening to a real amp, then you shouldn't use the USB amped outs, nor should you even record the Axe FX analog outs. If you don't give a toss about the AXE FX tricking people, and let it stand on it's own beautiful, new and larger-than-life-sound, then the USB amped outs are fine. The Axe-FX on it's own does not sound like a real amp...it has it's own sound, a sound many of us far prefer to even the best real amps.
The AXE-FX sounds too digital. Usually, when referring to software amp modelers, "digital" means harsh, stiff (from the early days of digital) and with that horrendous fizzy digital sounding distortion that *ALL* software amp sims (except the Axe FX) currently posses. When I say the outs on the Axe FX are "digitally" I mean new-school, high-end "digitally." Meaning, too perfect, too sterile, needing some analog "messing up" to sound like a real amp. However, this "digitally" is not bad in isolation, just different than the sound of a real amp...you might like the Axe FX "digitally" sound...it's pure, not harsh, organic and clean...near perfect...too perfect to be a real amp. The many analog byproducts that you're accustom too are missing.
Here is what we have today, from predictable > unpredictable.....digital>solid state>tubes>tape
If you want to fool people into thinking your AXE FX studio recordings are using real amps, you need to mess up the sound a bit. The AXE-FX amped output is too digital perfect. You need to add randomness.
These will help make the sound less digitally perfect and predictable:
-Tubes or analog before the axe FX like preamps or even a mild solid state or tube compressor
-Tubes or analog after the axe FX like preamps or even a mild solid state or tube compressor. This is what I usually do. At the every least, I run the AXE-FX outputs through some high quality analog EQ or compressor, tube being the least predictable and therefore best at hiding the digitalness of the Axe-FX.
In my world, if I wanted to record a clean signal in parallel to the Axe-FX amped outputs, I would use a high end DI to record the clean, then go to the Axe FX as if it was a regular amp. The Avalon, REDDis, Summit DIs of this world sound clearer than the Axe FX preamp and you eliminate an extra layer of conversion. Also, remember to run guitar DI thru signals to the guitar input of the Axe FX and line-outs out of active DIs into the line in on the Axe FX to avoid impedance mismatch darkening/muddying. With my Axe II, I will definitely try out the USB clean outs...can't wait!
Just like when we got CDs (besides the horrendous conversions until c.2000) digital sounded weird and unnatural to most...no hiss, no pops, no analog distortion glue, bizarrely punchy bass, etc. That is quite analogous to what the Axe FX delivers, (but without the bad converters) The note punch on the Axe FX is stunning! While the Axe FX can do a decent (relative word) job of recreating the existing, loved analog signal paths of traditional guitar chains, I emphasise looking at this a new way to listen to your pickups...don't even call it an "amp" maybe, but if you must, call it a digital guitar amplifier.