I just didn't think ports on the side was what people wanted, I've only heard people say they want it on the front so they can use it like a corded mouse, and I've never seen a wireless mouse with a port on the side before. Sounds goofy.
But if we're talking about the side... sure there is some room there, but I can see other issues like needing to have it be overly recessed due to the slope of the sides. More importantly it would look ugly compared to hiding it on the bottom... very un-Apple. Since the port being on the bottom is actually a non-issue for people who actually own a Magic Mouse, it's not surprising Apple would want to visually conceal it the way they do. But sure, Apple could move it to the side if they wanted.
It's just such a dumb thing to be worked up over. It literally has zero impact on you if you actually use one, unless maybe you are a robot that uses the mouse non-stop and doesn't sleep, therefore can't ever find 30 mins to recharge it.
So yeah I don't think bad design, its just a design that has some elements that are form over functionality, like most Apple products do.