I also noticed this, but it's not a huge deal. I just figure the 5D2 was extraordinarily fast starting up, and the 5D3 has more to do when it wakes up. The lens hypothesis is interesting though.
I simply extended the auto-sleep timeout (4 minutes? I forget my exact setting.), and I subconsciously tap the half-shutter button before bringing the camera up to shoot.
When the grip comes in, I'll probably be less worried about conserving battery power. The single battery has already lasted a ~2000 shot wedding, which is almost 3 times what Canon claims for one battery. So I'll probably extend the auto-sleep timeout even further and just use the lock switch when I holster the camera. I doubt there are any hard specs on power consumption when the camera is on but not doing anything, but it can't be too bad.