Linux

Yes, I love it and don't get me wrong but there are many downsides and they all result from poor planning and/or bad decisions around how flatpak was built. Here are a few:

• Poor integration with the system: sometimes works against you and completely bypasses your system instead of integrating with it / using its features better. To me it seems more like the higher levels are missing pieces to facilitate communication between applications (be it protocols, code or documentation) and sometimes it is as simple as configuration;
• Overhead, you'll obviously end up with a bunch of copies of the same libraries and whatnot for different applications;
• No reasonable way to use it / install applications offline. This can become a serious pain point if you're required to work in air gapped systems or you simply want to level of conservation for the future - it doesn't seem reasonable at all to have to depend on some repository system that might gone at some point. Note that they don't provide effective ways to mirror the entire repository / host it locally nor to download some kind of installable package for what you're looking for;
• A community that is usually more interested in beating around the bush than actually fixing what's wrong. Eg. a password manager (KeePassXC) and a browser (Firefox/Ungoogled) both installed via flatpak can’t communicate with each other because developers seem to be more interested in pointing fingers on GitHub than fixing the issue.

Flatpak acts as a restrictive sandbox experience that is mostly about "let's block things and we don't care about anything else". I don't think it's reasonable to have situations like applications that aren't picking the system theme / font without the user doing a bunch of links or installing more copies of whatever you already have. Flatpak in general was a good ideia, but the system integration execution is a shame.

I personally don't really like it, since it sidesteps what is supposed to be the all-in-one package manager for the system, and integration can be poor.

It's an alright idea, but I like the native package managers better. We're not Windows, we don't need so many different places to download our stuff.

There's still a few edge cases that Flatpak is not great for. The Flatpak version of Kdenlive video editor can't see Whisper, which it uses to generate subtitles. The Appimage and native builds work flawlessly.

I'm assuming these problems will be addressed eventually but it takes time.

• no OS level components
• duplicate libraries as some core apps (editor, filemanager, Desktop) cannot be flatpaks (yet?)
• old runtimes etc. dont force developers to keep them updated. Often thats because or 3rd party packagers though
• complicated packaging, I heard that the Flatpak builder is better for certain languages.
• theming issues I heard (on Fedora Kinoite Wayland it just works, and I can also force themes per app)
• bad permissions by default (best we have though)
• bad run commands (this could easily be fixed, and I have a script for it)

For OS components / packaging every part, Snaps may work, but for GUI apps they seem subpar and nobody really cares.

Nix may be way better for installing just anything compartimentalized, but there is no permission system (thats why packaging is easier).

But Flatpaks are really great overall, Bubblewrap, KDE Settings / Flatseal, Portals, official app support. Its really really important.

For me, the question is why I should add an extra layer of complexity. If the things I use already work well using apt, and if most things are bundled in the default distro install, then my life is already good.

This all depends on your software needs, if course. Some people are using a lot of new stuff, so the above setup leads to annoying situations.

There is some drawback. The main one : app can't communicate with each other.

Example firefox and his extension keepass. As keepass can't communicate with firefox, you have to open both apps and switch their windows.

You can use flatseal to manage communication between apps but that's not an easy process and may prove a security issue if you don't understand the technical jargon.

IMO yes but it might not be an issue for you, flatpaks work like windows standalone executables where each app brings all their dependencies with them, the advantage is the insane stability that method provides, the downside is the huge size the app will ultimately take, flatpaks are compressed and they don't really bring all their dependencies with them (because they can share runtimes) but the gist of it is a flatpak is usually much heavier than a system (.deb .rpm .PKG) package.

If you are ok with tweaking I recommend nix pkgs as they work on any distro and only take slightly more space than system packages. I have a terrible connection and low disk space, flatpaks aren't something I can use on the long run.

Oh and if you're wondering flatpak >>>> snap > appimages (IMO)