oops 0: Sorry I didn't reply to the list last time. (Ops, could that be made a default in the list management service?)
oops 1: You did ask about fonts too, didn't you. Sorry, I missed that and only paid attention to the color part.
oops 2: I seem to be having similar problems, and my previous suggestion is off base.
In the past when I've tried to fix this, one of the links that helped me:
...but not today, I notice that the changes I apply to my .Xresources file don't seem to make any difference. (Not surprising since the font I was using a couple of weeks ago is no longer appearing either.)
In my own 'term' shell script, a clumsy fix for the colors does appear to work, but doesn't address fonts:
#!/bin/sh
# 2015/12/11 after upgrade to El Capitan, settings in .Xdefaults or is it
# Xresources no longer apply, so this script is to make a terminal go
xterm -xrm 'xterm*foreground: rgb:a8/a8/a8' -xrm 'xterm*background: rgb:10/10/00' -xrm 'xterm*color0: rgb:00/00/00' -xrm 'xterm*color1: rgb:a8/00/00' -xrm 'xterm*color2: rgb:00/a8/00' -xrm 'xterm*color3: rgb:a8/54/00' -xrm 'xterm*color4: rgb:60/60/ff' -xrm 'xterm*color5: rgb:a8/00/a8' -xrm 'xterm*color6: rgb:00/a8/a8' -xrm 'xterm*color7: rgb:a8/a8/a8' -xrm 'xterm*color8: rgb:54/54/54' -xrm 'xterm*color9: rgb:fc/54/54' -xrm 'xterm*color10: rgb:54/fc/54' -xrm 'xterm*color11: rgb:fc/fc/54' -xrm 'xterm*color12: rgb:54/54/fc' -xrm 'xterm*color13: rgb:fc/54/fc' -xrm 'xterm*color14: rgb:54/fc/fc' -xrm 'xterm*color15: rgb:fc/fc/fc'
I'm sure there was an announcement somewhere in a recent upgrade notice, but I missed it.
And I sure would like my old font back.
After a lot of poking around, I notice the ~/xdefs-tmp/ directory has what looks like the new place to put this stuff. But the "tmp" makes me think they won't stick around. And, changes to files there don't appear to take effect, even after restarting X. (Not so surprising, since the .Xedefaults file I've been working with is just a symlink to there, and it hasn't been doing anything, but I thought maybe making changes to the XTerm files there might do something, and that doesn't do anything either.)
Oh well! I gotta get back to work. Sorry I haven't helped. (Either one of us.)