I originally thought the same thing yesterday when I first saw the pictures of the new Magic Mouse, that Apple had failed miserably on placing the lightning port under the mouse: the obvious problem being that it inhibits use while it charges.
But then I read about it being able to charge for 9 hours of use from 2 very small minutes. That to me is a great result. And if you think about the time it takes to open the battery slot on the original magic mouse when the batteries have drained, get replacement AA batteries from the desk draw (for me, anyway), then replace the batteries, clip the battery slot back in - that's about a minute or thereabouts. Plus, I then place the drained batteries into the charger and plug it into a power socket (a bit more time, albeit tiny). Not that I've really timed myself doing this but it isn't long, and so waiting 2 minutes for the new Magic Mouse to charge to an acceptable usage amount seems to add only a small amount of time to getting back a nicely charged mouse.
Force Touch inclusion would've been nice, however!
It's not that it inhibits its use, it's just not that, erm, elegant. You have to put the mouse on its back like a drunk turtle to charge it.