Yeah I definitely don't think everyone is going to like it. I used a community controller config for MGSV and then tweaked it to my liking. Basically, left analog stick for movement of course, with weapon and item switching on the left track pad (functioning the same as a D-pad). Left trigger soft pull will do the "aim," while a full pull will look down iron sights and activate the gyro. In iron sights, larger movements are still on the right pad, but smaller movements (headshots) are lined up using the gyro.
Didn't catch your edit:
That was fixed with firmware a couple of days after release. Now the desktop controls are fully configurable and work great.