Flatpaks bring all their own libraries with them rather than using the system ones.

• (plus) you avoid dependency hell, apps "just work"
• (minus) centralised version updates are less effective for bug and security fixes; all flatpaks must be updated separately
• (minus) all flatpak apps take additional disk space since they bring everything with them
• (minus) all flatpak apps take additional memory; Linux can't keep a single copy of a library read-only in memory if multiple apps are using it

I think they have their place for apps that are under very heavy development, or for apps which are extremely "resource heavy" in comparison to the system resources that they use (by which I mean, games). I wouldn't want my bread-and-butter system utilities to be flatpaks.