Hopefully the two series can coexist without too much problem. There should be some serious competition over the talent pool though.
Another thought, I wonder what Ducati and Aprilia(maybe Honda?) will think of allowing 1000cc in-line 4's into their V-twin party. I think Honda could switch over again relatively quickly, but for the two smaller Italian names, one who is in the GP's and one who is expressing interest, I wonder if they would continue to hold the same commitment to WSBK if they essentially had to switch to the in-line 4 configuration to remain competitive.
Here's hoping that the differences between the two styles of machines will be enough to keep good riders in each series... the more 2-wheeled sports the better.