The issues are twofold: Linux distros historically update software through a package manager. Something that was working fine for everyone, however it was causing a lot of work for maintainers. They got together and designed a packaging format for software that works across all Linux distributions called 'flatpak'. However, Ubuntu decided to create an alternative called Snap, which solves the same problem, except it's not used by anyone else.

Also, there's some implementation details that make it look messy in your system (every application is mounted as it's own filesystem, so if you use tools to list your disk's there's a bunch of weird spammy looking drives and things like that).

One of the things missing from other comments is the architecture of it, why it use to be slow, and how the binaries were handled. Canonical started Snap as a server oriented application deployment system, that has been adapted to desktop use with some technological debt. The differences between it and Flatpak as far as configurability, dependencies, bundled binaries, etc are somewhat nuanced. They dealt with the application speed opening issue by allowing decompressed executables and different hooks to be used.

The other main point of contention aside from technological debt inherited by a server-first development principle is how they closed sourced their Snap server backend. It's proprietary, while the Snap client is open source, how the actual Snap server runs is a mystery.

Flatpak (and by extension Flathub) are all open sourced, which aligns more with the philosophy that users tend to prefer. It was covered in other comments that everyone else uses Flatpak, and this really isn't so much as a debate between package managers vs Flatpak, but moreso of application deployment overall. The community prefers Flatpak, and Snap is pushed as a means of lock-in and sunk cost fallacy on the side of Canonical.