First off, thank you very much for this new emulator experience. It has breathed new life into these old classics. The real impressive part to me is how well the program is able to guess alot of the layout on it's own.
I have a lot to say so forgive me if I ramble a little.
More shapes:
I think a lot of users would agree that this is an area that needs expansion. What you have is a good start, but more variety would be welcome. Spheres, pyramids, half-shapes like half-cylinders or half-spheres.
Custom Shapes:
Even better than more shapes would be custom shapes. An editor to create or add your own shapes would allow better customization for games using less traditional side-on views.
Z Position:
We already have Z depth and Z scale, but it would also be nice to be able to set Z position, as well. The layer system kind of already handles this, but having just a front and back layer can feel too restrictive. Sometimes it can be difficult to get HUD elements to not be obstructed by level or character sprites. I don't know how big of a value would be needed. 0-255? Would 256 levels of depth be enough?
Sprite Groups:
While the emulator does a good job of grouping up sprites that belong together, it can sometimes make mistakes. The delete tool can help, but even that doesn't work, or causes more problems. Some examples are in Bionic Commando, some text sprites in the demo screen would get attached to a background sprite and deleting did nothing to help. In Spelunker, when trying to group the ground tiles together, every time I deleted some, it would effect others that I already fixed that I didn't select. Also Punch-Out is a good example since it has such large character sprites. Editing can give strange results because of the way the emulator decides to group them together.
I don't know how difficult it would be to implement, but a way to control what sprites are grouped together would be very helpful. Even being able to see how the program decides what is grouped together or what sprites are associated with each other would be nice. That way when you are editing, you know what will be affected by any changes you make. Of course that only works for whatever you can currently see on screen...
That's about all I have for requests for now. One other thing I noticed is that when setting objects to the background layer, setting their depth only seems to make it the depth go further back into the background. For example, if I have 2 objects set to the background layer, one with a depth of 8, the other with a depth of 32, the front face of both objects will be on the same plane and only the backs will be different - 8 and 32 respectively. Shouldn't it be the other way around so that the front of the objects stick out from the background at different depths? I can get that effect by fiddling with depth and Z scale, but it just seems overly complicated.
Another thing, like some others people have commented before, I thought it would be cool to have a sprite sheet option so that we could edit sprites directly from them. But then I realized why that is not possible. Take Super Mario Bros. for example. A classic bit of trivia and clever programming is how they used the bush sprites as cloud sprites or vice versa. You couldn't edit that one sprites values since it is used as 2 different objects unless you don't mind them appearing exactly the same.
Lastly, I would like to know what plans you have for expanding this emulator yourself. What is your vision for it beyond what it currently is?