I'm conflicted on this. I 100% think CLI applications should remain as packages but Flatpak IMO is superior for GUI. It just has a lot of "step in the right direction" sorts of things that address some of Linux's faults.
The big two positives for me are:
Makes it easier for developers to publish their own software and reach many distros at once. This has really helped with software availability and updates.
Sandboxing (although not perfect and Flatseal is kind of essential here, I hope this gets rolled into software centers or something).
I am on Fedora Silverblue and the concept of a base OS + Flatpaks just feels right for workstations. OCI containers (podman/docker/distrobox) as a bonus for development environments without borking your host.
But with this recent Fedora news (I know nothing has changed YET but I am just sussed out tbh), I am considering switching to OpenSUSE Aeon/Kalpa.
Your 2 big positives are stuff I agree with wholeheartedly. But I'm still holding out on using flatpak because it feels like an incomplete solution still. There's many things with it I could work around, definitely, but it feels annoying and with NixOS I don't have to worry about those issues because stuff just works for me.
As for FS, I wanted to love it, but doing some stuff with it is annoying. I wish it let you install stuff with dnf to /usr/local (like how it is on bsds or also macs with brew iirc).
Organizing my thoughs: I would love a future where flatpak just works, the sandboxing is nice and all you need is to click "yes" or "no" when an app wants/needs something, where you don't even need to use your distro's package manager (or you can't even use it because the distro is immutable and it updates on its own), but we're not yet there. Installing fonts on FS was a nightmare, and I had to layer stuff like powertop and other stuff I don't remember right now. Also flatpak isn't yet a good solution for development with VScode or similar stuff.