I have an Arcteryx Atom LT hoody that's my go-to mid-layer if I'm wearing a shell. It's feather light and the material feels great against the skin. Per your issues with layer multiple hoods, I sort of bunch of the hood and collar around my neck and then use the hood with my H/H Alpha shell. The material of the Atom LT packs down easily so it almost acts as a neck gaiter rather than a hood. It's breathes great and I've worn in subzero and on warm spring days and I never seem to get too hot or too cold.
With that said, I'm considering an AirBlaster Ninja Suit for my base layer. Apart from the bathroom challenges, do you like the one-piece set-up? I feel like this would solve the occasional, chilly, exposed gap between my bottoms and top when I'm riding a chair.