So, I give Cass a hunting shotgun, and she wont use it. I give boone Q-35 and he'll use that? WTH? Confusing game mechanics... Would just be much easier if you can tell them to use certain weapons.

You have to give them the appropriate ammo and Boone svcks at Energy Weapons; also, they go by the DPS, so if Cass has anything in her inventory capable of outdoing the Hunting Shotgun, she'll use it. The Q-35 skates by only because it fires faster than the hunting rifle.