This is interesting, because the last few days I was actually working on packaging an application of mine as a snap/flatpak.
From my PoV, they both have their fair share of issues.
Snaps enforce a sandbox, which I think is actually a good idea, because the desktop security model is somewhat broken. If your application cannot run as a sandboxed app, you need to be granted special permissions by canonical after manual review (my app needs this), where they also discuss if they can make a new permission in a safe way for your usecase that everyone can use afterwards.
On one hand this sucks because I need to ask canonical for permission to publish something, and there's no certainty that I will get these permissions as a nobody for a new app nobody ever heard of before. On the other hand, I think I like that they're doing something about the desktop security model.
The next problem is, if this is denied, how do I ship updates? Provide a self updater? Easy to write, but if everyone does that, we can just go full windows and abandon package managers. Tell people to just curl | bash? That's not more secure than a potentially shady snap.
But I do have to praise canonical for being very helpful in IRC and the forums for helping me debug issues and file bugs against snap stuff.
Now flatpak on the other hand, just feels kinda weird to me.
It sandboxes things, but every application can pretty much grant itself access to everything. This is a completely different philosophy, but if you rely on everyone tightly sandboxing their applications without granting themselves permissions for sandbox escape, I think something like landlock[0] (when it lands) or pledge is much more suited for this, and baked into the application.
Then there is this weird thing where flatpaks force a runtime on you. My application is a statically linked go binary. But flatpaks pretty much want to force me to add an entire freedesktop suite as a dependency, as you simply cannot choose no runtime.
(Community-)Support for building flatpaks? Pretty much non-existant.
So yeah, the entire linux upstream-packaging situation is still quite depressing honestly. And with the time and energy I have invested into this by now, I could have written a simple but sufficient self-updater about 10 times over.
[0]: https://landlock.io/
