I am working under the assumption that the transition will be similar to the transition from Math A/B to the "new" Integrated Algebra 1, Geometry, and Algebra 2 with Trig, i.e. that it will be cohort based and will NOT allow schools to wait an additional year, although that would be nice.
The attachment to this post is a slide show from the NYSED December meeting. On page 18 is the all too familiar block diagram of the CCSS transition timeline for New York State. In Footnote #3, it states, in no uncertain terms, that the transition will be "Cohort Based." I take that to mean that any student entering high school from September 2013 onward will have to take the Common Core based math exams and not the current tests. Those who entered prior to September 2013 will be elligible for the current exams. The only outstanding issue in my mind is the cohort that entered in September of 2012. I would assume that NYSED will mandate that this cohort must still take the new CCSS aligned Geometry Regents exam, but will have the option of the older Integrated Algebra exam or the newer CCSS aligned exam, should they fail the older exam.
I have heard no suggestion that students will have to take both the new exams and the current ones next year (other than on this listserv). NYSED does some very strange things, but this would make no sense and have no precedent in the last decade of transitions we've had to deal with.