I had the same issue; left-hand alt/option and command keys were sitting lower than normal, had lost most of their click, and were hit-and-miss when pressed (they required more force to register). My 12" retina MacBook is still under its initial 1-year warranty, so I took it in to the Apple Store. The Genius tried the keys and then immediately took it for repair; it was away from me for six days, but only because of a mix-up in ordering the new topcase (a US keyboard arrived, whereas I'm in the UK), which delayed the repair by 48 hours. The repair itself was done at my local Apple Store here in Edinburgh, Scotland - the MacBook didn't have to be sent away.
They replaced the entire topcase (contrary to how it sounds, that's the top part of the lower half of the MacBook, which has the keyboard and trackpad components). The entire keyboard was brand new and unmarked when the laptop was returned, and it's all working perfectly again. I didn't lose any data during the repair either, so the internal drive wasn't touched.
It it hadn't been under warranty, the replacement would have been £147 for the part and £24 for labour (figures from 28th Jan 2016; these were listed in the repair work authorisation email from Apple). As an interesting aside, apparently the most intensive part of the post-repair testing procedure is for the Force Touch Trackpad.
I've used just about every Apple keyboard from the last 20 years, and the new MacBook's keys are usable enough but a little too shallow. I think the new 2015 model wireless Magic Keyboard is the best keyboard I've ever used, though - with just a tiny gripe about the MacBook-like full-height left/right cursor keys. They make the up/down cursor keys hard to distinguish between by touch. I'm hoping Apple will go back to half-height left/right cursors again in future. It'd also be great if the next retina 12" MacBook had the kind of key travel that the Magic Keyboard has, but that'd probably mean making the laptop slightly thicker, so I doubt it'll happen.