SQL Server Compact you can enjoy benefits that Isolated Storage may not be able to provide you, such as using Plinq (Parallel Linq, see: http://msdn.microsoft.com/en-us/library/dd460688(v=vs.110). aspx)
I confess, I did not get to test Plinq in App for Windows Phone, but in relation to desktop really better performance when used correctly.
Another point, SQL server was made for this, storing large masses of data, while Isolated Storage, serves to save data for quick access, such as settings. However, what I think will really be the key point, is not where you will store the data but how you will handle it and at this point, I believe that SQL once again draws attention by supporting parallelism.