Wow, I've been away for too long... Its nice to see that someone else has picked up Xport's torch and is running with it. Most of what I'd like to see has been lightly touched on before, but here's my two cents:
1) The most important thing to add to any/all of Xport's emulators is the inclusion of some kind of crc/database to match rom file names with their "real name" (Fully spelled out name, no FATX cutoff, etc) and to match up screenshots/artwork. I still think that Surreal 64 has THE BEST way to scroll through games by box art rather than by listing. I and others have brought this up many times in these types of threads, but it usually gets ignored. Even if you yourself don't care for this type of menu layout, it could very easily be remedied by allowing for different "views" in the rom selection; much like XBMC has "list", "large icons", etc. For the package that you end up releasing to the public, you would use scaled down, low res icons just as Surreal does, but the user could then opt to download a high res screenshot pack (from XER) to allow for larger icon displays. The only issue you would have, would be deciding on how to deal with the two major romsets that most people would be using: Goodtools & the No-Intro sets. Maybe allowing the user to set this as an option in their gui settings?
2) This falls partially under number 1, but is mostly a seperate issue: Better/different screenshot usage/naming conventions. As has been mentioned by madmab, by default it seems that Xport's screenshot display goes by date, THEN by file name when displaying them. This gets fairly annoying whenever you want to update your shots, only to find out that you have to delete them all off the xbox, then transfer them all back over at once to correct this. Also the 0001.png and so on naming convention is pretty annoying. I think nes' approach in ZSNES with having different "shots" folders, and keeping the shots named to the rom is the better approach.
I also like having the "noob proof" setup available as well as most people here reading this may be fairly comfortable with the emulators, but hand the controller to your parents/kid/clueless friend and they'll have no idea what they're doing and ultimately screw something up. This is also where the box art menu selection really does wonders too.
I realize this is off topic, but as Vamp mentioned, emulators that handle multiple systems, even those that don't normally seem like it (Neogenesis for Sega Genesis/CD/32X) should really have multiple rom listings. Hell, maybe even have seperate launchers for each as it would be nice to have a Sega Game Gear themed skin for those roms as well as a seperate Master system one.
As for the base skin, I know everyone has their own opinion based on how their xbox is configured, but I really feel that Neverwill's approach on PSCXBOX is the best. Having animated representations of all of that particular system's mascots really makes it stand out. I mean for NES, have Mario, Zelda, Little Mac from Punch Out, an Excite Bike racer, etc. That would be wicked.