Why SQL Server 2008 R2 do full installation for just adding another instance on the same machine
Actually Sql server has two types of component\features.
1.  Instance specific features
2.  Shared Features
And Database Engine, Analysis Services, and Reporting Services are part of instance specific features which has to copy many files for installing new instance.

http://msdn.microsoft.com/en-us/library/ms143786.aspx