@IvCHo
2) I can’t understand how isn’t this annoying you 
I’ve used a lot of desktop environments (xfce, lxde, cinnamon, unity) and only MATE has this strange behavior. When I first saw it I thought “lol somebody forgot to put an Open With option”. Creating a custom caja script to open a selected file with pluma is much faster than opening pluma and searching for the file you want, or even using the terminal So, I insist that there must be an option “Open With” when you right click a .desktop file.
3a),3b) Indeed the developers must be really busy since they are doing really great job, but it would be nice to see these improvements for MATE 1.16 and Ubuntu-MATE 17.04. When you say the they “need to be requested” do I have to do anything? Or shall I wait for a mate developer to see this topic? I have no idea how features requests work.