My last two trips have been super short. They looked like this:
May 2015 (2.5 days): (stayed onsite at CBR, then switched to a Universal hotel after we finished at WDW)
Arrival day - headed straight to Epcot. Got to the park around 2:30pm. Toured Future World first, then WSC (snacked around the world for dinner) & Illuminations.
Full Day #1 - Pre-park open ADR's at Crystal Palace in Magic Kingdom. Then basically toured the park, commando-style, all day. We had BoG ADR's around 4:30pm so that was a nice sit-down break. We caught Wishes and closed down the park. I think we were at MK a total of 14 hours or something insane.
Full Day #2 - Rope Drop Animal Kingdom. Rode Everest x2, Safari, Dinosaur & Primeval Whirl. Breakfast ADR's at Tusker House. Saw Festival of the Lion King and left. Headed to Hollywood Studios, FastPassed Toy Story, ToT & Star Tours. Late lunch ADR's at Sci Fi. We managed to get on RnR twice, standby. Did some other wandering around but decided NOT to stay for Fantasmic, and instead went BACK to Magic Kingdom and closed down the park again. (Rode rides during Wishes, walked onto everything, it was great.)
January 2016 (2 days): (stayed offsite at one of Universal's hotels and spent 3 days at their parks as well)
Full Day #1 - Rope Drop at Magic Kingdom. Then basically toured the park, commando-style, until about 1:30pm. Had a sit-down lunch at Skipper Canteen (no wait). Caught Festival of Fantasy parade. Did "anytime" attractions, plus our Fastpasses from mid-late afternoon. Left the park before Wishes because we were FREEZING, but aside from missing the fireworks we were able to accomplish almost all of our must-do's. Grabbed dinner outside of the park.
Full Day #2 - Rope Drop Animal Kingdom. Rode Everest x2, Safari & Dinosaur. Had some quick service snacks. Saw FLights of Wonder and left. Headed to Hollywood Studios for lunch ADR and Mama Melrose (Fantasmic Dining Package). Rode Toy Story, Star Tours & ToT on FastPass. Met Darth Vader & Chewbacca at the Launch Bay. Did One Man's Dream. Had a butterfinger cupcake at Starbucks. Saw Fantasmic. Saw Star Wars fireworks (LOVED).
^^ We were sad to skip Epcot on this trip, but something had to go. With Soarin' down and new Star Wars stuff in place, HS was the best choice for us.
These trips were definitely a bit exhausting, but we accomplished all must-do's on both without a problem, and it was just enough to leave us wanting more and excited to return to WDW. My next trip will be a solo 5-day in September, and I am looking forward to a more "stop and smell the roses" approach. It will still be a relatively "short" trip but my touring plan will be much less aggressive since I will be more focused on enjoying my very favorite things rather than trying to do everything once.
Edited to add: A general theme you'll notice is we used table-service ADR's, usually for lunch, as our sit down mid-day "break" rather than leaving the park. This saved us a lot of travel time and I think it is a really good strategy for a short trip, as other have noted below.