What about using a bunch of Aldrin Cycler-esque designs which go between the different planets? For example, you could have one that goes between Kerbin and Duna, say with a crew of 8 (although the ship would need to support 16 for safety reasons). When the ship first arrives at Duna, the crew would land at a prebuilt base, and any existing crew would be picked up from the surface to take back to Kerbin. Then, back at Kerbin, a crew shuttle would be sent up to the cycler, where the crew from Duna would return home and a new crew could head towards Duna. Then, at Duna, depending on the transfer windows, you could have another cycler going from Duna to wherever works best next (say Dres). A few of the crew from the Kerbin-Duna cycler could wait on Duna until the Duna-Dres Cycler makes it to Duna, and then board that cycler to land on Dres. It would take a bunch of surface bases and giant ships, but I think it would avoid a lot of the stress problems and a lot of the problems with solar storms, since the crew would mostly be on the surface of different bodies.
