hey there,
i was linked here from func_, so i haven't read any of the posts. i'm just responding to the OP.
vital:
-map limits: i won't bother listing them all, but essentially, if i'm able to compile the map in aguirRe's tools, then it should be loadable.
i consider fitzquake to be adequate (although i have already reached the limits in v085 and had to scale back a couple of maps).
if fitzquake double it's limits from 085, i would be very happy.
also: don't neglect the max_ambient_sound_channels (or whatever it's called). i'm talking about that error that shows up when you have a lot of ambient sounds in your map which stops further ambient sounds from playing. fitzquake still uses the old limit (or the increased limit is still too low)
-multiple mod loading. especially for quoth because it sucks that anyone who made a map back when it was new essentially had to dump their files into the quoth folder.
fitzquake has -quoth but dp does it best, i think, with a more general method of just specifying whatever mod folders you want in a row.
-the signon buffer and whatever else needed to load up maps with tons of entities.
-alpha transparency with the .alpha key for windows or whatever. it should work on everything; brush models, mesh models and sprites.
not vital, but Pretty Damn Important:
-skyboxes and fog: while not having any impact on gameplay, skyboxes contribute a lot to the atmosphere of a map and not having access to one or both sucks.
-i would also consider it pretty important that there be a qc manner to load fog and skyboxes. if you have a map that used multiple skyboxes or fog levels, it shouldn't be necessary to have to use fancy qc to get the settings to stick for map loading and saving.
-external file loading for map textures, sprites and skins. this opens up all new texture sets for use in maps. (but pretty much everyone does this already)
would be very nice to have:
-sound sources that move with entities they are played on. so my lifts and trains emit their sounds nomatter where they are after they started.
-going along with the previous point, doppler effect.
-stereo sounds
-ogg support
-real rotating brushes. i'm so damn tired of that hacky hipnotic shit.

if this was a standard, it'd be beyond cool to have proper rotation.
-some way to have more control over particle temp entity effects in qc. it doesn't have to be complicated.
say for example, you take all the currently existing temp entity particle effects and give the ability to control what colours are used by specifying a start and end point on the palette.
and maybe a way to scale the size of the particle effect so you could have a TE_EXPLOSION at half size or something.
so.. yeah, that'd be my ideal quake engine standard.