Apple should have employed the services of Logitech who actually know how to design a mouse for the productive worker, with comfort being the prime directive.
I have two MM gathering dust in a drawer they are so good.
So if Logitech makes great mouses for you, why should Apple have them build one with an Apple logo on it, instead of you just go out and buy Logitech mouses?
If there is a different mouse out there that works better for you than the one Apple makes, why are you stressing out over the details of the Apple one instead of just happily using the one that third party makes?
In any case, I think mouse ergonomics are not as cut and dried as some people here think they are. Are you holding the mouse wrong? If it is causing you discomfort or pain, yes, likely so. If you just aren't comfortable with it then it could be that you just need a differently shaped mouse.
Apple mouses are not and have not ever been (at least in the post-hockey-puck era) designed to be held in the center of the palm like one would a Microsoft or Logitech "ergonomic" mouse; they have been designed to float at the fingertips. And, yes, if you are constantly picking your mouse up you need to adjust its sensitivity settings; that isn't a comfortable operation with any mouse, but especially not the type that Apple sells.
So far as ergonomics go, the golden rule is that you need to make sure your wrist is kept straight both horizontally and vertically while operating the mouse. Personally, I find this easier with the small fingertip mouse or a trackpad than with the big bulbous "ergonomic" mouse designs (for those to keep my wrist straight I need an elevated wrist support, which I find uncomfortable). But, if that is the mouse design that your hands need to maintain a straight wrist then you should be looking at those designs. There are dozens if not hundreds of companies making them, with at least a good five or six quality efforts to pick from. Hell, Microsoft puts an "ergonomic" label on its "wedge" mouse which is intended to be held and used exactly like the Apple magic mouse, so if you feel you need an "ergonomic" label on something without carrying a big plastic bulb around in your laptop bag, there's even that option for you.
Some mouse makers claim that a "vertical" grip is better from an arm comfort perspective, but that seems to be completely not backed up by any scientific study. That said, if having your grip vertical like with a joystick is significantly more comfortable than having it flat like you are typing on a keyboard, then there are a number of options out there for you with that design as well.
All of which is to say that a good number of people find the Apple mouse design to be really comfortable to use. It isn't because we just made ourselves get used to it; it is for the same reason as there have always been a variety of mouse designs - various people find different ways of holding a mouse comfortable. If you don't like "flat" mouses, then look to other more full-spectrum mouse designers and see what Microsoft or Logitech has to offer. I won't tell you you're deluded by thinking that bulbous ball of plastic is comfortable if you'll show the same respect to me.