Hmmm, a few features I would like you guys to consider are the following:

1) Sideview ladders (given the variety of scripts at PureZC are either broken or don't have all functions to work properly).
2) Sideview water (because why not?)
3) I'm not sure if this would directly affect the engine, but another request would be expanding the Palette table to use more than just CSets 2, 3, 4 and 9.
4) Lastly, a few new items wouldn't hurt, like the Pegasus Boots, Shovel, and such. I know they're already existent as scripts, but I feel they would work better being hardcoded in the engine, because by doing this, you can save a lot of scripting space, flags and misc. Plus, sometimes setup is a bit quirky, especially when you want to combine them with other scripts.

So far, those are the only things that I could come up with.