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It makes it easier to package and install stuff once and for everyone. And harder to keep your system patched because some software might include older versions of libraries. And you can't just install the patched version from your system repo, because that doesn't apply per design. We also have some minor woes like theming, filesize, integration into the desktop... I think it isn't the best we have right now. I think that is system packages. But that depends on the specific use-case. Yeah. But we need both. At least as of now. Maybe we'll one day get a more unified package format. Or sandboxing for almost everything like on Apple computers. There are some limitations. We can't have everything at the same time. But there is lots of room for improvement. Linux is awesome, though.
I agree that an officially supported system package is the best option, when it's available. But I'll happily install a flatpak if that isn't the case. And yes, it would be great if we could get a universal standard.