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.

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.

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.

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

i never have issues with flatpak

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?

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.

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.

the apt version.

My personal rule of thumb is that if it interacts with the OS or filesystem deeply, native is probably better. E.g. IDEs, cli programs, browsers, Steam etc.

Apps that do a simple things are likely to work perfectly fine on flatpak.

But the problem is that there are outliers in each case. You should pick one and be ready to switch if things don’t work properly.

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.

I’d go with the Debian package. That’s tied into the system. You get nice updates, there’s more eyes on what the upstream developers do, sometimes the Debian maintainers disable things like tracking, fix vulnerabilities in libraries. It’s smaller, less permission issues… It’s just safer and more convenient…

I’ll go for Flatpak once there’s some benefit. For example the sandboxing which is great to have for proprietary software. Or if the package isn’t available in the Debian repositories, and the alternative would be some third-party repo or deb file downloaded from a random website.

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.

Before going to Flatpak just for newer versions of software, consider APT pinning. You can actually use testing or Sid packages on more stable versions of Debian while still keeping the advantages of Debian-specific packages.