Has anyone explained the cause of the discloration? It's possible that whatever caused it could be a factor in the concrete's overall, long-term performance. Your builder conveniently forgot a very important fourth option--complete removal and replacement of the discolored concrete.
That's what I would demand, considering it's a new house. You shouldn't be required to put up with stains or skim coats that will eventually wear unevenly, possibly debond, and result in a lot more problems down the road.
Get a few quotes from concrete specialists for complete removal and replacement. Then suggest to your builder you would be happy to have the work done by one of the specialists if he is unwilling to do it, provided he will pay for the work, of course.