I'm awaiting the new AE before I delve into scenes, however, I've gotten around the situation you describe by assigning all of the X/Y choices to one CC#. So I have a generic X/Y IA switch on my MFC. I can pick and choose what I want to change. If a block is to remain unchanged, I just copy it from X to Y. If I don't want to use a block on X, but I do on Y, I just zero out the mix on that block in X. Combined with 2 pedals set to control various modifiers and a mixer block, there's very little I can't accomplish with this setup. If I'm concerned about a seamless transition for a particular song, I make sure I use two (or four) parallel chains with the mixer block(s) tied to a pedal. I would say I use this setup on 75 percent of my presets.
I do something similar now as well. The Mixer blocks are incredibly useful, and take up very little CPU. I wish we had a few more, and wish the final Output Mixer was also able to be controlled via Modifiers.
All in all the control available in the Axe II is awesome, so many ways to accomplish your goals. I will eventually use Scenes I'm sure, but the shared Modifiers for x-y states limit what I'm able to accomplish. This was no different before Scenes were introduced, but still limits control too much for what I do now.
Currently to work around this, I start my chain with a Wah and Phaser block, but split from there into two parallel chains. Each contains a Compressor, Drive or PEQ, Amp, GEQ and Filter Block.
Filter Block is set up using an Envelope to control low end.
The two chains come back together in a Mixer block that is hard panned L/R and feeds a stereo Cab block, this way each Amp has it's own Cab.
I have one amp for Clean, the other Dirty and use an Expression pedal assigned to a Mixer block to sweep between Clean and Dirty tones.
The two GEQ's are assigned to one IA to handle lead boosts and are tweaked to best fit the Amp being used. I also assign modifiers to same IA to increase Delay and Reverb for solos. When the Solo IA is active, I can use the Expression pedal to have a Clean or Distorted lead tone.
This gives me 4 sounds, Clean, Clean Lead, Distorted Rhythm, and Distorted lead with just one IA and one Expression pedal. I still have the other IA's available to pull in whatever effect I may want to add as well.
I split the chain again toward the end to run Reverb and Delay in parallel into another Mixer block to keep things a little cleaner.
Doing this has allowed me to use a single preset for an entire song instead of switching Scenes or presets. I will use x-y occasionally for Delay block, but have found with Amps and Drive blocks especially, the switching is too obvious.
I'm certainly open to suggestions though, if anybody has a cleaner way of doing it I'd love the input!