1- It takes a lot of space. jUsT bUy a bIgGeR dRiVe --stfu I'm not going to spend money for you to waste it
1- a) Everyone assumes you're an American with 20Gbps symmetrical fiber optic. My internet can't handle 2+ Gb downloads for a fucking 50 Mb app bro
2- Duplicate graphics drivers. Particularly painful with Nvidia
3- It puts a lot of security work with distro library trees straight into the shitter
4- Horrendously designed system for CLI apps
(flatpak run org.whocares.shit.app
)
5- Filesystem isolation has many upsides for security but also it can cause some pain (definitely nitpicking)