Ok, lets try explain these OS X specific changes (given it's my fault they happened).
There were two OS X based default key changes. First was default remapping of fine controls, from Caps-lock to Return (Caps lock doesn't register for some reason).
The second was exposing the shift+scroll wheel to zoom in editor (it used to be hard coded to shift), and then giving LeftCommand as default for OSX. With external mice, Shift+scroll never worked to zoom in editor as OS X uses shift+scroll to horizontal scroll, and so Unity never picks it up (and just uses it as normal scroll I think). With track pads and Magic Mouse, it worked fine, because they don't have the shift to toggle horizontal scroll thingy. LeftCommand was chosen because a) I'm right handed so I like it on the left of the keyboard, b) LeftAlt is the mod key (eg alt+F12 etc), c) LeftShift only works when using trackpad/Magic mouse (maybe some others with special drivers or something) and d) Control is used for OS level zoom to cursor by default.
From memory (can't check currently) normal scroll in flight zooms in/out, middle mouse pans up/down. Until the focus camera 'tweakable' was implemented, there was no stock way to move focus from centre of craft. You just had to fiddle with zoom and pan to get the view you wanted.
