at a time I was in a quest for a global equalizer, and ended up installing an equalizer for pulseaudio. a little "cheating" to get a bit more bass and slightly less aggressive treble. it was not very easy to find and went unmaintained by its author, made the sound a bit "dirty" too. (similar to "issue with older versions of PA" you described).
but even with PA - couldn't someone just write a compressor/limiter/leveling amplifier for PA? (in some mixer utility) this hardly sounds like a case, where we need a complete re-write of both kernel and user-space sound APIs to accomplish... if i remember correctly, isn't it also possible to do this with ALSA/dmix too?