have you ever tried to place a green scream before your Wah while using an overdriven amp?
What about compressors - I usually place them before the Wah.
IMHO the "Wah using a stomp block" behavior ist just perfect as it is, cause it opens up way more possibilites.
of course Wah should stay available as a stomp!
Thinking a step further, it should not be very hard to program the "wah in rig setting" to be placed at any place in the signal chain