I think these could be fun. Of course it should be possible to turn them off. Some ideas below.

For starters, bring back the Falling Cliffs from MKD. I loved that stage.

MK9's bridge. Cars should sometimes head your way from offscreen, requiring you to either jump to avoid them, or destroy them.

The subway: It should be possible for fighters to be knocked into the tracks, and for the fight to continue there. Players could climb back up. The stage hazard is a no-brainer.

The cavern from MKM: Holes should sometimes appear on the ground, and those who fall in them will get impaled.

The pit, in 3D. Imagine if we could have fought on the actual Pit in MKD, or the narrow bridge in the Deadpool instead of that platform. 3D gameplay on these stages would require players to avoid sidestepping, as well as special moves that involve it. If Motaro came back as a sub-boss, such a stage would be ideal, as his attacks would be much harder to dodge.

Finally, the Pit Bottom, in 3D. Spikes everywhere.