Honestly, the only thing I will miss is the escape button but that was misplaced on the keyboard anyways. 10.12.1 added support for making caps lock into an escape key and that's if anything an improvement over where escape was before.
There is also a solution for Hammerspoon users here: https://gist.github.com/arbelt/b91e1f38a0880afb316dd5b573275...
Anyone looking for extremely fine grain keymap control (with a UI that far surpasses any kind of keyboard remapping I've tried doing in Linux) should look up karabiner.
in all seriousness, switching the ctrl - caps lock keys was probably the best layout improving decisions i've ever made. highly recommending it for ergonomic and health reasons.