I like the MK3 stages, but the UMK3 stages are pretty lame, maybe only Scorpion's lair and the Cave were any good - but all of them seemed out of place, whereas the MK3 ones were all around the city or Kahn's fortress.
My fave MK3 ones:
Smoke's portal - because it was the one stage (at the time) that wasn't part of the storyline, kinda like Goro's Lair in MK2. It was more like an MKII stage.
Pit 3 - I liked Shao Kahn's throne, the stone heads in the background, and the stage fatal.
Soul Chamber - just really cool, the soulnado and the shadow priests in particular.
Subway was cool, as was the Rooftop, and the Bridge and Street seemed to fit the vibe of the game nicely.
My all time MK3 fave is one that never made the game in its entirety unfortunately, and that's the Bank concept from MKDA's krypt. The helicopter crashed into the side of the building is perfect for the MK3 aura, and it's a shame they didn't put it in what turned out to be an otherwise bland arena. Couldn't find a pic of the sketch on the net, anyone have one they can post?