I will point out that while it's mostly the same as the SC2.0 system, there are some slight tweaks here and there. Mostly, it's been streamlined, with a lot of rules trimmed down for more streamlined play. However, if you have the SC2.0 book, it's fairly easy to port over any of the rules there that you liked to Mastercraft, or take a look at Fantasycraft and see what's different and make the same changes back to SC2.0 for your home games.
As of right now, Crafty Games plans on supporting both systems, with anything that should be stand-alone being Mastercraft, but things that are obviously Spycraft supplements still using the SC2.0 rules. Some things may have some crossover potential, and will be dealt with on a case by case basis (the rest of Spellbound, for example, is being released in PDF as SC2.0 the whole way, but will see print compiled and converted to Mastercraft). You can be confident that people on these forums will convert pretty much anything Crafty releases to the other system within a few weeks (their results should end up on the Wiki, but that can get neglected sometimes. The Liscense to Improvise forum is your friend).