In the 90's XMen cartoon, nefarious government agents used the Mutant Registry to test their super awesome mutant hunting mechs on, just for the sake of testing that the mechs could hunt down capture mutants that were registered.
So much for Humans + good Mutants vs bad Mutants theory... But then again, it is a Cartoon.
But unless the Government can promise that Mutants on registration wouldn't be needlessly prosecuted/persecuted, there should be no talks of said registry.