When I played my first Innsmouth game (no other boards) , I had an interesting idea:
I placed the Dunwich and the Kingsport board below the Innsmouth board so that the four other worlds were visible, and used all gates and gate cards from Dunwich and Kingsport. It really worked well, there was a gate to Lost Carcosa and one to the Underworld, and I even drew a specific encounter for each of them in the 3 investigator game.
If you know some problems that can occur (cards refering to expansion locations, rifts etc.), I'd like to hear about them. I'm especially interested wether you think they might be a problem, or wether you know it for sure.