OK, most would be double I think without too much issue. Lets start with Top-Down, it technically does support it. If you click "Use as a token base" it just places the overlay as a background image. There's a few square/hex overlay samples (I believe that come with it) that are solid for this use case. And of course, other bases can easily be added by the user.
As I mentioned, I had not used this in a long time... so what I'd be looking for is a slider to set the base's transparency to make it a little more useful. The current transparency slider does not seem to work when using "Use as Token Base".
Lmarkus' example of a background image and an overlay is what I was thinking about earlier as well. But I'd like to be able to set the transparency of the background image separately from the overlay.
So you'd basically have to have the ability to set up both an overlay and background image at the same time. And you'd probably have to have some "crop" options for the background to make it appears to be a "fill" for overlays (circle, square, and hex should cover most needs).
Some UI improvements. Since I can see a large asset library (which you want in order to make the program more useful) becoming unwieldy:
1) Have a visual display of current settings in the big window. For example, when using the transparency slider that is there now you only see the effect in the side side panel window. And then when you save token all it seems to save is the overlay. When using "Use as Base" it does nothing. Knowing what the final image is going to look like before I save it is kind of important.
2) Have separate lists for Overlays or Backgrounds so that they didn't come up in one list (i.e. a "Manage Bases" option).
3) Be able to create subfolders in the Manage Overlays/Backgrounds tree. For example I might have a folder for "Stone" and inside "Stone" have "Worked" and "Unworked".
4) Or, instead of 2 & 3 above, be able to tag the overlays/bases with some descriptors and then when "Managing Assets" have the option to display the genres and types that you want when picking them. Three basic fields would probably be a good start:
Field 1-- Type : Background/Overlay
Field 2 -- Genre : Contemporary/Fantasy/Horror/Military/SciFi/Universal
Field 3 -- Element : Earth/Stone/Metal/Organic/Liquid/Misc
Elements could be broken down a lot more but there is always a balance when having tags and search field between making finding something easier and making tagging too complicated.
And, finally... if I may... why not have this built into MT so we can create tokens on the fly in our games instead of loading up a separate program, creating the token image, saving it as an rptok file, then loading it into MT, etc. If you want to get people out of Photoshop/Gimp that would be a big convenience for in-game use and when setting up games. I guess I wouldn't expect you to put much time into this now... but maybe when Mote becomes open source you'd consider tackling that?