For me, if I could wave a magic wand, and change any two things about the look & feel of MC on Mac it would be (in this order):
1. Menus: The menus should be native, or look and work like they are native, including putting the proper options under the Application Menu.
This is the thing that makes MC feel the weirdest to me on my Macs. Otherwise, it fits in as well as many of my other "not quite native AppKit" applications do (which are many, including Office, Chrome, Firefox, and all Adobe applications). But, the menus stand out like a sore thumb.
2. Keyboard Shortcuts: It may just be a case of making the default keyboard mappings better for an out-of-the-box Mac install, but I think it is a little more than just that, as discussed above. In my everyday usage, ⌘-W is the most dis-congruous one, but I know these kinds of things stand out to many Mac users.
I also think both of those things can be done. I'm not sure about the work involved in #1, but I think it is important.
Are there other ideas? If you were given a magic wand and and able to choose only two things (where they can't be huge sweeping changes like "re-write the whole UI to be X," but limited-scope, targeted changes) what would you choose?