Unlike google play, apple's appstore and canonical's Snap, flatpak isn't limited to a single repo, apps from other repos will show up in the store ui just like any other app.
App stores are gatekeepers, and while they certainly can make things more convenient, they also encourage habits that I think are harmful. Such as thinking that app stores are the only way to install applications. I think that it has been a bad thing that users are conditioned to think that if it didn't come from an app store, it's dangerous or wrong somehow.
It forces developers to use the app stores. I understand that many may not see this as a problem, but many developers (including myself) would very much prefer not to have to do that. So it's a disincentive to make software for others, at least for some.
In the case of this one, I also am very nervous about the incorporation of a payment system. I fear that will discourage the creation of quality free software, and I think quality free software is a huge benefit.
In short, I fear that this app store will resemble the Android Play store, or Apple's app store, and encourage the same problems and adverse impacts they have had.
I hope, if this succeeds, it turns out to be a good thing.