I really think they need to do a total tear down of both sides and just come up with one layout much like Disneyland has with side-by-side seating so that capacity isn't lost. They could do what TRON has and have a two load stations (think Big Thunder Mountain), that way trains are always loading and trains are always departing onto the track.
I like Disneyland's version, but I don't know that I would want it to be a carbon copy. It's a fun coaster, the only thing I don't like is that it's mostly turns (a TRUE wild mouse) whereas WDW's has 2-3 drops, which is why I enjoy WDW's more despite DL's obviously being of higher quality.