ok since the atari emu's do not seem to be getting any loving. I'll go ahead and dive in with a first post.
Does not save screen shots correctly (colors are way off).
Sound emulation (old) has weird artifacts.
New is ok, but it is a whole octave higher so it sounds odd. In fact I dont even bother using it despite the sound artifacts that exist in old.
I dunno the story behind the problems you ran into with sound, but you may be able to get some help over at the Atariage Forums
there are some very knowledgable people over there and even a few emu authors frequent.
If you consider upgrading to a new core, just stay away from the most recent one. It breaks alot of things. But the one before that is fine. (I'm referring to Atari800win)
5200 controller mapping is a pain in the butt. With a little work alot of this could be cleaned up. See idea further below.
Farily accuratel autodetecting file types would be possible as well. Executable files have a (255,255) header and disk images, cartridges, etc have different headers too. I'd have to tinker with it a bit but most 5200 games use only 2 of the ROM types and 1 or 2 use specific ones. I could research more into this if you are interested in adding this.
Ability to save which disks where put in drives (1,2,etc). Keep in mind drive one needs to always default to selected ROM. I think this was 1st implemented in winuaex. Save state may have to remember what disk was in what drive.
Not sure if this did not exist until winuaex, but it would be kinda cool to be able to combine multi-game disks into one zip and then have the emu ask which (disk) to use when picking the zip (or inserting disk in drive).
A suggestion that would apply (and be specific) to several emulators would be some pre-defined setups. I know on winuaex some were made for default amiga configs.
In this case I'm specifically thinking of controller set-ups. A default for 5200 controller, standard atari controller (with space, enter, esc, start, option, select mapped), keyboard control (pad mapped to arrow keys on atari keyboard, button for space and enter). As an example, for standard atari controller I usually map select->back, start->start, and option->black or white, space/enter to x/y respectivly, esc to either black or white.
Of course user defined mappings would be even better. If interested I could work up mappings to the 5200. The only disadvantage is the 5200 controller actually has a numeric pad as well. Only a couple programs really use the number, most use the standard ones listed in your documentation.
Keyboard control defaults would probably be more useful to other computer emulators than atari. I have found, though, that most cases across the board the same keys are usually used. So it definetly would be handy. Respective fans for each system could probably tell you more about common keyboard setups on other computer systems then I ever could.
The ability to assign controller 1 as being plugged into port 2. There are probably only three games that require this, but it'd be nice.
Thank you for your time.