You know, this one should be obvious: IDs for collapsing scenery. That way, you could have platforms that go at once.

A less obvious, and probably tougher one: loops, and the events that go with them. People routinely use Layers 3 and 4 for their level layers. Loops could easily use a second masking scheme for Layer 3, with a 'side switch' event that could be placed near the top of the loop. The only thing that would be more difficult are sprites, but how hard could it be to make a set of walking/running sprites that are rotated 45 degrees (the other 6 positions could easily be made with clever use of flips and mirrors of the other 2 sets)?

Other, more outlandish ideas include:

Doing away with the clunky 32x32 tiles. 16x16 is the way to go. There'd be alot of tileset space saved, especially in tilesets that rely heavily-to-solely on other games' graphics, which usually use 16x16 or even 8x8 tiles.

A 'Custom Bridge' event. Using the current bridge 'engine', be able to use your own art (designated in the tileset, or just where the event is placed) to be able to create your own 'sagging bridge' graphics (even better would be if it were to use the 16x16 tiles, or have it split a 32x32 tile into left and right halves to create the effext).