to be specific just like wolfman pointed out: "nearly all themes there are small niggling issues"
That's a bit vague...
Another thing why people are going mint instead of ubuntu is precisely this, GTK 3 themes should work. In my case the menu bar indicators almost never match the themes.
But Gtk 3 themes do work. When they have issues in Mate, like the wrong color somewhere, it's an issue with the theme, not Mate. The same goes with the indicators: they're handled by the icon themes.
That's why I was asking for precisions: most of the issues you'll have are dependant of the themes and can't be fixed in Mate. Other issues can, like changing the logo on the menu applet: the applet Mate uses doesn't allow this, so it could be updated to have a new dialog to select an icon and such, it's part of Mate.
I agree about the wallpapers part, some work can be done here (at least drop the Mate logo everywhere and the green tint). Also, the background manager should be able to handle standard dirs (I already complained about this).