I have exactly 2 presets (three if you count my acoustic preset which just gets routed out to my Fishman preamp).
Clean with more or less grit & effects spread across all 8 scenes, and a dirty patch similarly set up.
Perhaps this is one of the reasons why I am such a fan of the FCB1010 as a foot controller. When you only need 2 pedals for presets (okay, 3) and 4 for scenes (each toggles between 2 scenes), then you still have 2 expression pedals and 3 foot switches that can be assigned to other stuff. It pays to be simplistic
Initially, I had only ONE master preset, as the OP talks about. Trouble with this was, since I use Axe Edit III to edit, it was causing glitches because the CPU was almost maxed out. There is definitley NOT "unlimited" CPU power - that's for sure. In fact, I regularly come into the 80%s and 90%s with what I feel are fairly basic pedalboard & amp setups.
In any case, I'd rather ride the 60%s CPU and have Axe Edit III respond somewhat quicker than try to cram my whole gig into one preset. Two is perfect. I may branch out more if I ever get inspired to sound JUST like the band we're covering, but as it stands, I just sound like me playing those songs and I'm okay with that