I have come to a similar conclusion regarding models in the AxeFX and my actual tube amps. Like you, I've gotten rid of one or two amps over the last year of owning an AxeFX because the models were great and I rarely played the actual amps, so made sense to just stick with the model and let the amp go.
For example, I own a real 1970 Marshall Super Lead but coincidentally, there is also a 1970 Super Lead model in the AxeFX. I had Jeremy from Ground Zero spruce the SL up for me and really bring it to life (no actual mods, just different component values) and so I went into the Axe FX and made the same exact changes (for example, adding a 4700pf bright cap). They're literally 99% identical now. Now, I'm not selling my SL because I love it, it's a collectible, and I enjoy owning it and playing it, but the AxeFX makes you sit there and wonder sometimes.
One thing I'd really like to see is more models added. They've been pretty good with it recently, putting in the Marshall Studio Plexi and the Revv, but would still love to see other rare amps, stuff like:
- Rev C/D/E Rectifiers
- Naylor Super Drive
- Friedman Naked
- Carstens Grace
- Carstens Warm Machine
- More obscure Marshalls (e.g., Vintage Modern, 1986 Bass Spec Plexi, 30th Anniversary, JCM 900 SL-X, etc.)