First off: use a stable platform, yet modern platform for development.
Such as Ubuntu. As you can safely bet that it has a stable gtk version. As when gens linux was actively under development a year or two ago, I couldnt use it because gentoo is on the absolute bleeding edge, this is bad when developing something meant for all distros as many may not be up to date yet, and no suggestions to converto to gentoo, as for some people, that isnt viable. (as not all of us have fast computers or connections)
Embedding the window using libgtkgl or glarea. I'd suggest taking a peek at visualboyadvance's gtk ui for reference on the sdl portion. (just for the love of god, dont use gtkmm like they did)
Support for playing things from the cdrom drive would be awesome. Shouldnt be too hard as media players like totem can do it. (simple as accessing the system's cdrom device, actually)
For netplay, I dunno. Unless there's a free and open (as in opensource) gaming network out there somewhere that can be used, if found, good idea to replace kaillera with this on all platforms.
Freedesktop standards, for kde and gnome menu entries, that way gens can be accessed from all freedesktop compatible environments.
Using png and xbm files instead of windows bitmaps and windows icon files. (png would be best as it can be loaded on windows as well.)
If I could actually sit down and code, I'd help.
The fullscreen support is nice.
Some reason, the SDL version moves slowly on my system, gl moves faster and better (thanks to the geforce mx4k card I own)
however, sound has a lot of clipping at 44100 hz. maybe be corrected using something like libmad for playback instead of incorporating mpeg123 code? Dunno if that would help.
Also, I realise gens is being overhauled with cleaner code, maybe some of these suggestions can be applied?
Distribution format for binaries: Autopackage (http://www.autopackage.org
) similar to windows installer. if a user doesnt have autopackage, they need not to be root. the autopackage backend will install and then install the package. pretty slick.
Then third parties can make .deb files or .rpm's and whatnot for those who must have such things installed natively to their distribution.
Default directories for savestates,screenshots, and whatnot under ~/.gens/
Gens would make a great genesis emulator (and does) under linux.
Still would be one of the better linux/unix ports of an emulator with these suggestions.