We've done short trips quite often. Usually for three day weekends. We've even done shorter trips.
What we would do in the this situation is to go to start in Animal Kingdom one day and MGM the other day. Do those until we feel we are "done". We don't do everything, just our favorites and maybe a few things we haven't done in a while. Then we end up in Epcot for the rest of the day. Since we usually go during a holiday three day weekend, we avoid Magic Kingdom all together.
I suggest that for your two days, you break it up into four different "areas". Saturday morning/afternoon, Saturday afternoon/night, Sunday morning/afternoon, and Sunday afternoon/night. We don't list what we want to do, just go with the flow. Like at MGM - if we can fit Rock N Roller Coaster and Twilight Zone in there, great. If not, we try for Rock N Roller Coaster first and Twilight Zone second. Then we just fill our time in with other stuff. Mission:Space is a must at Epcot. Flights of Wonder is a must at Animal Kingdom. Everything else is on the fly.
We might make one ADR, usually for a lunch.