The GoldenEye mod plays MUCH differently than under RetroArch; it plays more like the original game than Doom. This is because PrBoom Plus can read DEH files (either separate or imbedded in the wad). I would recommend anyone with a DEH wad try it in this version. Note that the patched RetroArch wads won't work with the standalone; you'll need to get them off a Doom wad site.
Upgrading the PrBoom core is definitely something the RetroArch team should consider. But I realize that they have so many cores that it's hard to concentrate on just a few at a time.
From what I can tell,the only RetroArch wads that have DEH features are GoldenEye and Batman, although I suspect that Half-Life and GhostBusters are too (they have flickering sprites). The first level of Batman isn't beatable in RetroArch; there is an enemy that drops a key when killed, but since only a DEH patch can make a key-carrying enemy (I think), the player can't get through the level.
Here is a link for these wads, if anyone is interested...
My testing shows that most of the mods seem to utilize DEH features (usually internally), but usually all they do is change the text that appears onscreen (map and object names). Sometimes they tweak the enemies' attributes a bit.
There is a cheap way to get RetroArch wads to work in PrBoom - rename them to one of the main Doom wads (doom, doom2, plutonia, tnt). This may result in graphical errors or other oddities, though. Most of the mods can be found on the site I listed above, others will have to be Googled.
I was just looking at all of the cores in RetroArch, and I wonder - what systems are left to emulate? Other than N64, PS1, Saturn, etc. But seriously, what's left? I mean, WonderSwan? Never heard of it (aren't all of its games in Japanese?) How about some of the oddball Mednafen cores: Virtual Boy, Lynx, Neo Geo Pocket? Or some really retro systems like Atari and Commodore 64 (a bit before my time, though)?
The most "popular" system that RetroArch could probably emulate is the 32x. Now before the snickering begins, consider this list: Panasonic 3DO, Philips CD-i, Atari Jaguar, Nokia N-Gage. Ugh. Are there any other source ports like PrBoom for other PC games? Now DosBox would be interesting. The PS3 port is a bit clunky and underpowered; it'd be nice to be able to play more powerful games like Quake, Duke Nuken, and Grand Theft Auto that PS3 DosBox can't. But I suppose coding a joystick, mouse, and on-screen-keyboard into RetroArch wouldn't be fun (PrBoom ought to have an OSK but doesn't).
So other than updating/improving current cores, and adding a MAME core based on a slightly less ancient version, what's left for RetroArch to do?