One of the biggest issues of running a custom kernel is that you are taking a vital piece of your system out of regular updates. This means that you need to manually install all kernel updates from this point on. These include additional hardware features as well as critical security updates.
This can be a problem if you need a system that runs and maintains itself with minimal user intervention. As such, running a custom kernel not only requires you to know what kernel features you want but also be aware of critical updates.