I felt the need to compare two databases and I thought of trying out the Compare Schema feature. Surprisingly I was not able to find it out at all, and then my real issue started. I did all I can to figure out what would be the real cause of the same, and I also felt into a suspicion that, it can be the case that SQL Server 2008 R2 might not be supported by this tool like it was with SQL Server 2008 in the GDR 2 release. Out of my impulsive nature, I also posted a query on the forums.
Finally, I figured out a small point which solved this entire puzzle. The installation was of "Professional" edition !! You might not be able to figure out yet, what it has to do with this issue. My feeling is that VSTS 2010 Professional Edition is almost a paralyzed edition for DB development using VSTS. If you compare the database development features available in Professional vs Premium/Ultimate edition, almost no features of DB Pro are available. Check out the feature comparison between these editions from here.