I have the same issues, I had the same problem in the beta and was very pleased to see that the loading/saving times were much improved in the final version, but as soon as I had a certain number of companions (I think it was the 6th) the loading/saving times increased greatly. now I am afraid to accept more companions, will it get even worse?
has anyone tried to empty the inventory of unused companions? it really is next to gamebreaking, I love the game, it's far better than I hoped for, but I just don't feel like playing like that. a first countermeasure would be the possibilty to disable autosave to zone transition is at least less painful.