The custom controllers are handmade to order by a third party that has to pay the full retail price of the original controller. Not to mention the fact that they're grossly overpriced as well.
Even back at launch when economy of scale hadn't kicked in, the Xbox 360 wireless controller only cost about $10 to manufacture. It was overpriced as well, but the margin was necessary to offset the large loss that they were taking on the console itself.
Assuming that none of their existing manufacturing chain was reusable and that somehow the new controller costs five times as much to manufacture, that's still a gigantic profit margin. It's not like the console itself isn't profitable now, either.
It's grossly overpriced and exploiting the market, plain and simple. The fact that they've put the remappable buttons behind an artificial software barrier really evidences that.
We'll see if it's grossly overpriced soon enough, in which case the price will drop. Econ 101 Dwell, if people want it at that price they can get it.
I don't understand freaking out about this sort of stuff.