I wear the Patagonia Nano Puff w hoodie as a mid layer on colder days. The hood fits snugly under my helmet and is super comfy. You may need a little extra room in your helmet, but with the thickness of the hood on the nano puff it's not an issue for me. There is no vision obstruction like you might get when using the hoodie on your shell or outer layer. It seals in the back of your neck and I zip up the front to provide some face coverage. You can still use the vents to release the extra BTUs when needed.
I know, it's pretty dorky, but most of the time you wouldn't know the hood is is under there. There have been mornings where I roll out of my sleeping bag with hood up, throw on an outer layer and the helmet and I'm good to go.
That said, the nano puff is lightweight for a mid-layer. If you really want a cold weather set up, I'd recommend looking at a heavyweight base layer with build in "scuba-like" hood combined with a non-hooded insulated mid-layer under your outer layer.
As far as outer layer hoodies over the helmet go, I like a hood over helmet for the lift ride, but I won't ski with it up. I agree - hood over helmet restricts sensory perception and should be avoided.