The FIM Superstock bikes have much more factory backing behind them. All the major ones are putting forth their best efforts. The MA series is slightly skewed since Graves/Yamaha are the only ones that have the dollars to push development and setup. Which essentially proves that in reality, they are all close enough that all that matters is which one gives you the biggest boner.
For those that haven't been able to watch the FIM Superstock 1000 races this year, I'll host them so you can download them. Just give me a few hours to get them set up. It's really intereting to watch and the Eurosport announces are way better with technical details on the machines, riders, and teams.