Having root doesn't necessarily mean having a custom ROM... I just manually root the stock ROM.
I use a few apps that require root, but I need the stability of the stock ROM. Since I'm still stock I can flash any system updates that come along.
I was stock rooted on my Nexus 4 for months too, custom ROMs are nice and I applaud the developers who work hard on building them, but I don't need the extra bells and whistles, especially when they occasionally cause instability.
First thing I do with every Nexus is unlock the boot loader, flash a custom recovery and flash supersu... Manually, of course. Toolkits are no fun.
Sent from my Nexus 5 using XDA Premium 4 mobile app