I disagree. Flatpak pros:

- installing: easy to locate, install and has centralized management for updates.

- flatpaks are also persistent. User-installs are in the home dir.

- sandboxing built-in.

Can't comment on other stuff. Haven't had issues.

sandboxing built-in

This is both a pro and a con. For example, one big downside of this approach is that it can make installing third party plugins and scripts much harder than it should be.