Going to OP question (I'm late to the party here)....
1) no this FW update won't mess up your presets or alter them significantly (unless you are still on FW 9 or 7 or something). Minor tweaks in a few places. I am really finding myself more and more leaving the amp at default and just tweaking presence, drive, master volume, maybe bright switch and moving the treble/mid/bass knobs by no more than "1" from default 5 except for a few amps that love otherwise.
2) everything sounds and feels right/better (no steps backwards here or recreating presets from scratch). There is no way in blind test of mic'd cab vs. AXE II that 99% of people could tell the difference, the Marshall-style amps for example are just frickin' outrageous and I love the new jumpered amp models.
3) cab IRs are becoming where it's at to get the last 10%+ of nailing the tone. Had a tone I was chasing, my old Bogner Ecstasy 101b into a Bogner 1 x12 dual port Shiva-type cab. I shot IR's last weekend for it (and my Bludotone cabs too) and *BOOM* there it was for the Bogner Amp model and the BludoOjai. Lots of flavors too for bright, balanced, or dark (bass) from multiple mic shots for IR. Do not neglect the cabs, period; try lots to get the sound you want -- it will "click" and you'll hear it.
If you don't think the AXE II sounds like your own real amp of same thing, then truly learn how to shoot Cab IRs' of the speaker cab you love/use; it it still incredible to me that the AXE II has this power. I'm going to shoot some more cabs with a Fathead (R121 style mic) and SM57 over the weekend.
Honestly, if it never got any better than the current FW and Cabs, I'd still be thrilled and have enough to play with to last me years. I mean, we all now own 128+ modeled amps, that never blow up or need new tubes, right?