I don’t think we should change the default apps in this cycle. Our primary goal is to provide the good old working unity desktop with most things intact. We are already recommending gtk3-nocsd for unity-session. The advantage of gtk3-nocsd is that it is customizable for users even at per-app level. I am planning to add that information on wiki so users can easily find it.
About mate equivalent apps, I agree with 1,2,3,4,5.
gnome-screenshot → There are issues alt+printscreen, worse with mate-screenshot.
totem → I prefer
gnome-mpv. It has inbuilt settings whether to use headerbar or not.
The current issue with mate-apps are mate dependencies and mate prefixes. I already had conversation with @Wimpress about this. Mate team is removing prefixes and improving on dependencies issue. But I don’t think it will happen in this cycle.