It depends on the use really.
If I was watercooling, the Prodigy would be my choice.
If you're wanting an incredibly compact rig, then the CM Elite 120 may be under consideration.
Personally, it would take a lot for me to go smaller than a Prodigy. I just think you give up too much in terms of upgrade-ability and cooling options to give up the Prodigy for something smaller. I've not properly seen what the new Bitfenix cases are like (built on the same chassis as the Prodigy I believe(?)). Depends if you like the exterior design more I guess.