Hmm if the models were previously ok regarding their thickness, then FUD should do just fine. As for the sprues, I didn't know that worked, I thought Shapeways would then consider it a single part, thus making it more expensive? Man, they can be confusing sometimes!
But maybe you can already start by selling your stuff in FUD. (a) it's a bit cheaper, and (b) the quality is superior to the flexible plastics. As for updating the models themselves. No need to hurry there, wouldn't surprise me if Shapeways will end up changing that as well!