I know, we're working on getting a new system into place. This one is cumbersome. We want to incorporate all new features and Facebook connect so you don't need to login to comment, etc. Hopefully, this summer :)
The islands are the main play areas and the goal of the game. But there will be some time spent traveling from one to the other. There must be or the supply line strategy would be useless if you could just pop from island to island.
And I agree, sitting in the RTS mode for the whole game would make one miss some of the truly cool stuff in the game.