He already announced this at Comic Con. Yes, Xavier's consciousness did survive the events of X3, but he didn't transfer it to the body of his brother and he isn't currently using his brother's body.
The actual film NEVER established that it was Xavier's brother. That was just some offhand commentary by Brett Ratner. It doesn't HAVE to be canon.
Singer has explained that a certain mutant recreates Xavier's body after X3 and Xavier transfers his still-living consciousness into his original body. Those are the only details we have, but this will be the original Xavier.