Technical stuff aside, a major reason why Flatpak does not get the hate Snap does is because users don't resent it.
There are 2 things people hate: the way things are, and change.
Ubuntu put Snaps on users desktops without asking if they wanted them. They just did it, then closed off ways to opt-out/avoid them (Cf. Firefox).
Forced change fosters resentment.
No distro made Flatpaks default/required/opt-out. Users had time to come to the tech and adopt it on their own terms/needs.
Just IMO.
If you try to use Flatpak as a developer outside of GitHub and the usual programming languages and outside of a corporation, stemming the costs, you may realize, that it is the same walled garden like the rest.
And that is, why I rant about Flatpak, technical stuff aside.
But they don't directly spit into our faces, at least. That is reason enough for many people to trust them. 
And people want to have a magical wand, which solves all our problems. "The unified Linux desktop!"
The hunt for it lets some of us forget, what we are really here for. Creating a diverse world of tools for everyone.
Not everyone at once. - That would lead to some of us left behind.
Besides that, a magical wand is worth huge risks for some, which will ruin it for many of us.
omg! ubuntu
AdeptVeritatis