When comparing yay vs Flatpak, the Slant community recommends yay for most people. In the question“What are the best Linux package managers?” yay is ranked 8th while Flatpak is ranked 18th. The most important reason people chose yay is:
It's written in Go so it is fairly easy to add features or tweak this amazing tool.
Specs
Ranked in these QuestionsQuestion Ranking
Pros
Pro Easy to add features
It's written in Go so it is fairly easy to add features or tweak this amazing tool.
Pro Intuitive CLI
Yay's commands and output make sense for anyone used to the pacman package manager.
Pro Written in Go
The compiled program is snappy while the source is easy to read.
Pro Available as a precompiled binary
Both yay and yay-bin are in the AUR, the latter of which doesn't require any dependencies or compilation, making installation and updates quick and painless.
Pro Yogurt interactive mode
Write package name without keys [yay <packagename>] to enter interactive mode.
Pro Doesn't rebuild already-installed apps like Trizen
Pro Cross-distribution
You can install flatpak packages on any distro you want.
Pro fast
searching, installing and updating are faster than others in my experience
Pro Doesn't bog system down like snaps.
Plus it's not proprietary.
Pro Application sandboxing
All applications are limited to a set of predefined permissions, enhancing privacy and security.
Pro A well-written documentation
Pro Flexible runtime management
You can install a lot of runtimes for different apps, making applications a lot more compatible while still allowing some applications to share their runtimes.
Cons
Con Written in Go
Running a Go program requires the Go runtime. Go is also a garbage collected language, so the program isn't as responsive as it could be.
Con Bloated
Due to the way Flatpack handles packaging, this can lead to a large cache being created which quickly inflates to unreasonable sizes. Not only this, but using flatpack requires a large chunk of space to be reserved for it's own file hierarchy.
Con Difficult to export packages
It is difficult and convoluted to export installed packages and move to another system.
Con Doesn't work well with CLI programs
Invoking CLI programs can be a pain. From the weird reverse DNS package names to difficulty in easily managing container environment.