The one reason not to go with roll top panniers is accessability. You have to dig through the whole thing to get things out. I have Arkel panniers, and love them even though they are not "waterproof". Only once have I found anything wet in them, and that was from riding in a lot of standing water on the highway in a downpour. Non waterproof bags do breathe some, so anything wet going in has some chance to dry out, unlike in waterproof bags.
I would agree with your reasoning of using only front bags with the trailer, as you will have enough weight on the rear already.You may not need to replace the crankset to get the gears you want- my touring bike (not tandem) I changed the chain rings out, going from 52/42/30 to 48/39/24. You will appreciate having lower gears at some point I'm sure.