I haven't tried the new OpenEmu yet (just the early betas), but the file management was what made me drop it.
You see, I've got a meticulously-arranged archive of stuff, with custom icons on the files, associated box art, attract screens, in-game screens, posters, manuals etc. When I throw all that at OpenEmu, I had the experience of it only recognizing some of the files (I've got custom ROMs I've built myself), un-grouping variants, only being able to handle certain compression formats (for some systems, I have all the ROM variants in one 7z archive with the default being first in the index with the earliest name). This archive took me a good 10 years to build, and has survived through many emulator attempts, so I'm not about to abandon it for a single emulator

When testing OpenEmu, I quickly discovered the "large library" error, and so tossed my test samples at it (for each emulator it can handle). Even then I had some difficulties with compression formats.
It'd be nice if OpenEmu itself would transparently recognize zip, 7z, lza/lzh, gzip and bzip (plus the iso compression formats) and for any format it doesn't recognize, run the command-line version of the unarchiver at it to see what can be found.
That's my two cents

It's definitely showing lots of promise though.