I've had this same problem with my Missions as well.
Your Proto VR's have a stiffness rating of 5.5, this is middle of the road as far as stiffness goes with the Mission line.
I've only used the VSI proto line, and they have a stiffness rating of 7.5, so your skates should break in a little faster than mine did.
What I did to solve the "pain" issue was to leave the laces across the top of the foot a little loose, then when you get to the ankle area you'll have to crank them down. You'll have to experiment with how loose and how tight you make the laces, but this does work.
I'm not sure if the VR's come with waxed laces or not, but this really helps keep the loose area "loose", and the tight area....well, tight. My VSI's have the heavy duty waxed laces on them (Mission has the market on the waxed laces! ) they're a pain in the butt when the skates are brand new, but well worth it for the painless skating.
If you are using regular laces and try this tightening method, the slack from the top of the foot will find it's way to the tightend area around the ankle and then you're always retightening, and there will be a little pain still.
After a while of doing this, you'll notice that you'll start getting the area on top of the foot a little tighter, untill the skate is completly broke in.
I hope this helps.
