I would go with Debian package but for me the primary consideration is how much I care about having the latest version of given software. Often I don’t really care that much. Although it needs to be said that I’m on Debian testing.

Stable package > back port package > flatpak/snap.

Basically I want everything as stable as possible unless I have a particular need for a newer feature.

The main things I run from flatpak/snap are browsers and the Minecraft launcher because they are both regularly updated.

For desktop things, appimage is my preference. Then flatpak then debian repo.

For cli things, if its a really old school low level utility then debian repo, otherwise nix.

IF the distro’s .deb is recent-enough, THEN go with that.

IF it’s generations out-of-date, then you may have no choice but to go with the flatpack.

OS-integration ( with apt, for the .deb ) is to be preferred, generally.

_ /\ _

Heuristic : if you don’t know, trust your distribution. If you don’t trust your distribution, pick another one, repeat.

Usually native packages are preferred, unless like you said you want a newer version. Some people also like the sandboxing that flatpak does if you don’t fully trust a program. The reason why the flatpak is so much bigger is because it needs to download the dependencies as well, because it can’t use the ones on your system. In this case since it’s a game it probably needs graphics drivers as well, which are fairly big i think.

Go with deb package if they are both the same version.

I run Debian 13 and I will use apt repositories whenever possible and I avoid flatpak with a passion.

My flowchart is:

1. App Image if the application supports auto updating or if it’s a temperary app
2. Apt repository
3. Deb file
4. App Image (when previous didn’t apply)
5. Source
6. Flatpak

My main reasoning for it is strictly ease of use. I find flatpaks while I’m sure makes it easier on the developers making it to be super bloaty and take up more system resources, While causing more restrictions and annoyances during configuration due to their enhanced security setup.

The only time I really don’t use a repo if it’s available is if the program itself updates on its own, or updates super frequently such as Discord, which I got annoyed enough at that I had to make my own update script that to check if there’s an update and then auto update it, because I got sick of the Discord has an update message every other day.

Sometimes it’s specific to the application. As an example, yt-dlp is redistributed by Canonical, and they usually maintain stable packages, but their versions seem to lag like 6 months. This might be related to their desire for stability, or maybe just align to their release cycle. I don’t know.

The issue is that yt-dlp needs to be updated more frequently because websites break their methods of downloading, so the version that follows the latest version seems to work better.

I don’t think using PPA’s is usually recommended, (like in the photo) so I think I would recommend flatpaks first if the developer of the application maintains one themselves. (and you want to follow later releases.) Though, the first time I had to use flatseal to fix an application, I felt like flathub was a failed platform.

Of course it would require password, you’re putting something into your system after all. Arguably, Flatpak has some layers between it and your inner system.

What di you mean your distro’s repo is an untrusted source? Did you do something funny to it?

i never have issues with flatpak

You might also consider linuxbrew as well, depending on your goals. AFAIK it’s almost the same as native but with better separation of dependencies.

I’m still not a Linux expert myself, but I’m gonna take a shot at answering this question as I understand it so maybe others can help correct me. I use Arch (btw) but the ideas should still apply,

You’ll want to use the Debian packages for anything foundational to your system. These packages are tested to work with the distro and can be considered a part of it, just ones you haven’t installed yet. This would be important for something like bluez bluetooth (or whatever Debian uses).

Aside from the space issues you mentioned, this is less important for heavy apps that sit on top of everything else, like a game. Especially if you’re on a slower moving distro like Debian this may be ideal for more updated versions.

Usually I go: distro repo (HIGH PREFERENCE), AUR (not really an option for you), Flatpak, AppImage, whatever other jank manual install is available (but only as a last resort if I really need the thing and there’s no other option, I like a tidy system). I find this offers the best stability and as someone who obsessively updates their system every day because they’re a bored tech nerd, I’ve had better stability on 3 years of Arch than I have with Windows (but that’s a low bar)

I generally prefer system native packages to flatpaks, just cause I’ve had a lot of issues with flatpak permissions. I suppose for something like a tux game permissions wouldn’t matter much lol

I’d say if the version is the same, go with the Debian packages and then fall back to the Flatpak one if it doesn’t work.

The 260MB of storage for Flatpak is a bit misleading though. If you have other flatpaks installed, it’s smart enough to deduplicate the files and share them.

Another thing to consider is xdg compliance. If you’re really picky about having a nice clean home directory and the program likes to vomit files into it, Flatpak keeps that contained in its sandbox. Not something to worry about for most people though.