You should read this:
A minimal and trusted set of repositories: given the aims and goals of Kali Linux, maintaining the integrity of the system as a whole is absolutely key. With that goal in mind, the set of upstream software sources which Kali uses is kept to an absolute minimum. Many new Kali users are tempted to add additional repositories to their sources.list, but doing so runs a very serious risk of breaking your Kali Linux installation.
As for snaps and flatpaks, that is up to you, just as it was on mint (AFAIK they do not force any of that on you with mint)
And mint is not a rolling release, it’s a point release, you SHOULD reinstall.
Flatpaks etc… IMHO f.ex flatpaks is a great way for devs to minimize work but at the same time make the software available for all environments able to run flatpak. If you want to package something not available on f.ex apt, you are still able to compile from source, but then obv not get support from the devs.
And as for wayland, well. If you want to live in the past, go ahead. There is a reason close to every distro out there is switching to wayland.
But since default DE is xfce on kali, I don’t think you will be forced to use wayland any time soon.
See: Wayland | Kali Linux Documentation
There is a meta package for MATE on kali: kali-meta | Kali Linux Tools
But as for MATE, they are also moving in the direction of wayland…