The Xposed framework has opened up some interesting mods. Most of them do only a few things. Some of them do a lot more. GravityBox does a lot more than that. This module from XDA Developers member C3C076 (keep 'em comin, guys) seems to incorporate all the little tweaks that people generally flash a custom ROM for, but it's built for stock Nexus devices and "clean" AOSP ROMs.
Here are a few of the highlights for GravityBox: PIE controls that replace the on-screen navigation buttons.