When comparing GNU Guix vs Funtoo, the Slant community recommends Funtoo for most people. In the question“What are the best Linux distributions for desktops?” Funtoo is ranked 32nd while GNU Guix is ranked 58th. The most important reason people chose Funtoo is:
The profile system improves portage's usability without losing the soul of Gentoo.
Specs
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Pros
Pro Can setup a shell which has exactly the defined libraries available
A method which works across languages and provides a reproducible programming environment.
Pro Can always roll back to a safe state
Guix creates new profile generations for each operation. If anything goes wrong, a simple --roll-back gets you immediately back to the previous, working, generation. Because it is a purely functional package management system, generations don't affect each other, so you're back to the exact same state as before : still working.
Pro Can create independent packages
Guix pack creates packages which do not need Guix to be run.
Pro No side effects when building packages
Guix is a purely functional package management system. This means that the act of building a package does not have side effects, such as destructively updating or deleting files that may be used by other packages.
Pro Can build containers right-away, from docker to tarballs
See guix pack --help and here.
Pro Easy to add your own packages
The clean and declarative syntax makes it easy to define new packages by using an existing one as an example.
Pro Doesn't require root privileges
Normal users can install packages on a Guix-enabled system, or even run their own Guix instance if the system isn't Guix-enabled.
Pro Like Gentoo but more streamlined
The profile system improves portage's usability without losing the soul of Gentoo.
Pro Use flags that are suitable for a task or environment are grouped into Profiles
It allows selecting, for example, gnome or desktop profile with most of the sane use flags enabled inside the profile.
Pro Portage tree split into kits
This allows more fine-grained control over package updates, and packages can be now tied together inside the kit to minimize dependency breakage while upgrading.
Pro `boot-update` to take care of bootloader configuration
A tool to update your grub config.
Pro Funtoo Linux offers a variety of stage3 builds
Customized to a variety of CPU microarchitecture variants from AMD, ARM, and Intel.
Pro Stage3 sources are built using the Funtoo Linux tool 'metro'
It's a sophisticated replacement for Gentoo's build tool 'catalyst'.
Pro Uses GIt instead of Rsync
THis makes updates so much faster!
Pro Stage3 archive coming with pre-compiled kernel based on Debian's kernel
Pro Simpler template-based network configuration
Cons
Con Updates take a long time
It's gotten better over time but both updating Guix itself and updating the installed packages can take a long time.
Con Cannot handle filetypes that have different semantics across different versions
While the functional approach that Guix takes is great for sandboxing binary artifacts of packages, it seriously lacks any power in handling configuration files or user data. It's difficult to upgrade and downgrade files where semantics and syntax can change between versions.