OK, so on the subject of the FBA CPS-2 and Neo Geo cores and their regression in compatibility for 3dsx users, aliaspider said this was due to increased RAM usage of RetroArch, which should become less of an issue once ninjhax & friends 2.5 are released and allow more RAM in homebrew.
However, in the meantime, this means a number of large-ish ROMs which used to work in these cores no longer do, such as the X-Men/Marvel fighting games on CPS-2 and Metal Slug 2 on Neo Geo.
Since nightlies on the buildbot only go back to October 13th (seemingly after RAM usage increased), it's hard to tell when exactly it happened. I don't grab nightlies every day, so the next-most-recent version I have on me is 2015-10-02_RetroArch.7z, on which the Marvel games and Metal Slug 2 work. As such, I'm attaching the cores from October 2nd here.
It's very likely that there are somewhat more recent nightlies which still work for running these games, so if you've got a nightly between 2015-10-03 and 2015-10-12 which works for these games, you should probably use that instead (and maybe upload it for the rest of us if you feel like it).