I am currently using Linux Mint (after a long stint of using MX Linux) after learning it handles Nvidia graphics cards flawlessly, which I am grateful for. Whatever grief I have given Ubuntu in the past, I take it back because when they make something work, it is solid.
Anyways, like most distros these days, Flatpaks show up alongside native packages in the package manager / app store. I used to have a bias towards getting the natively packed version, but these days, I am choosing Flatpaks, precisely because I know they will be the latest version.
This includes Blender, Cura, Prusaslicer, and just now QBittorrent. I know this is probably dumb, but I choose the version based on which has the nicer icon.
I too have been using native packages for 25 years and I wouldn’t say it have been “fine”.
I’ve had to deal with outdated packages, where to have the latest version of a software you had to compile from source.
I had to deal with 3rd party repositories that broke my system.
I had to deal with conflicting versions of a library.
I had to deal with the migration from libc5 to glibc and God that was horrible.
So yes containers might be a little more complex in its implementation, but it means I can install apps from third parties without touching my system and I love that. My OS stays clean, and my apps don’t mess with it.
It’s not that I’ve never had any problems. It’s more that those are infrequent one-time problems, and if something happens once every two years that takes me 30 minutes to solve, I’m willing to do that if it makes the day-to-day use of my system smoother. Flatpak feels like I’m rubbing just a little bit of sandpaper across my face 20 times a day, and the promise is, “yeah, but look how you’ll never have to solve this minor one-time things again”, and that’s just not a trade I want to make.