Atmosphere will want a customized implementation of the Horizon Kernel.
Atmosphere should have a set of tools designed for debugging.
For user's benefits, we'll likely want custom sysmodules -- both of the Rosalina style to extend the kernel/provide new features, and of the loader re-implementation style to hook important system actions.
Patches will need to be developed for Horizon to implement desirable CFW features.
In the absence of a released coldboot entrypoint, Atmosphère will want to support backing up and using virtualized/redirected NAND images.