Another issue I've had with Snaps is just increased boot times. Something to do with mounting all the virtual images involved or something, makes boot take noticeably longer. I've tested having an Ubuntu install with Snaps, and then removed the snaps and snapd while installing the same software via Flatpak, and had a noticeable boot time improvement. Hopefully they've been working to improve this, but it just soured me on them even more.

As for another install method, mostly for CLI tools, but working with a lot of GUI apps too now, there's Distrobox. It has a bit of a bloat issue, because you're basically installing an entire extra headless Linux Distro with it, but it for example allows you to run AUR inside an Arch based Box, and then you can integrate the app you installed with AUR into the host OS, running it near seamlessly, while keeping its dependencies contained in the Box which you can easily remove. By default apps in the Box will have access to the host's filesystem but you can mitigate this if you want. Distrobox is especially great on atomic read-only Distros, where you can't directly touch system directories, by allowing you to install apps that expect such access from things like AUR.