Best improvement so far is switching from Darwin cube to Mendel A-frame.
I think the addition of a heated build platform to control warping and eliminating the need for a 'raft' is a major upcoming design improvement.
If the RP'd rack & pinion drive works out, and eliminates the need for expensive timing belt, that will be a big step forward in self-replication.
On the software side, incorporating the MakeNBreak.py feature (multiply in vertical stacks) into Skeinforge would increase production speed of RepRap parts.