The current trend in the Android mod world is to make everything systemless. With the systemless SuperSu and systemless Xposed, you can finally switch back and forth between a stock and a modded system in just one click, allowing you to make OTA updates or just have a clean system without hassle.
After trying a couple of Android ROMs for my Nexus 5, I decided to go back to stock with XPosed (mainly because of the Cataclysm ROM‘s dev stopping working on it).
I was used to do everything manually via adb to have total control, but a couple days ago I let myself be tempted by the powerfull Nexus Root Toolkit. And powerful it really is!