I use ThinkTank holsters deep enough to hold body and lens with hood in shooting position. I generally don't use front caps on my 70-200 2.8L II and my 17-55 2.8. The hoods always stay in the shooting position.
Granted, if I need both lenses, I carry two bodies and avoid changing. But, on occasion, I'll carry just the 7D with 70-200 and a 35 2.0 for wide shots (ok, normal shots on crop). I would carry a single holster with side pocket for the 35. It helps to have one pocket or bag dedicated to each lens so you don't have to swap them out. When I change lenses, camera strap is around the neck, body is tilted down to avoid dust. The mounted lens is removed and straight to the holster or side pocket, hood first. Second lens rear cap removed and transferred to first, second lens then mounted to body.
Things were a little easier with the old FD lenses. One could use the thumb to flip the rear cap off into the camera bag, then mount to the body one handed while still holding the first lens in the other hand.
Oh, for smaller lenses where I do use front caps, I use Tamron caps. They are similar to Nikon and much easier to remove than Canon caps. (There's no way I'm putting a Nikon cap on my Canon...just can't do it.)