Did you already try adding all the mobile user agents to the “Rejected user agents” list in w3tc?
I use this list for this purpose (not created by me and certainly not complete but enough for my purpose):
iphone
ipod
ipad
aspen
incognito
webmate
android
dream
cupcake
froyo
blackberry9500
blackberry9520
blackberry9530
blackberry9550
blackberry9800
webos
s8000
bada
That’s a common workaround that almost anyone uses to have w3tc and WPTouch working together.
*Edit* You wild need to reformat the list to have one per line to insert it in w3tc.
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