I've found it's either just that it's a lack of support issue aka not enough Linux users for that product or service to justify support or good support. Either that or whatever I needed was a project run by a single guy so it works kinda but also kinda not.

I guess one issue I used to run into particularly in development was conflicts in setting up a lot of things. Now with atomic systems and a sandbox for all my dev tools alongside snapshots that's essentially dealt with. Also flatpaks can be a massive pain in the rear if one wants more direct CLI control or is getting other issues with the sandbox of the flatpak format.

I was really into the VanillaOS project for a little while but it's somehow gotten worse instead of better, at least the last time I used it earlier this year.