I'm using a Rockman Midipedal. Since I'm mainly a bass guitar player and not really a guitar player, I never had a pedalboard so my approach to midi presets/control is different from others. I never thought of enabling/disabling single effect.

The Rockman midipedal is a simple 5 preset with bank up/down controller. Each of my banks have switches for clean,crunch,rythme,lead and wah presets and each bank is targeted to the music style I want to play: acoustic, blues, rock, hard, metal, shred. If I need specific effects for a song I create a bank for that song, or for that artist. So if I want to play blues I go to that bank and I have 5 presets to play with.

Since the wah has it's own preset in each bank (because I also change the amp eq, delay and reverb) my expression pedal (an old converted Crybaby) is setup for volume in other presets of the same bank, so no needs for 2 expression pedals.

With that approach, you can use a cheap midi controller without fancy programming features as you only need PG messages.