Do you think my changes in the server (enabling .NET 3.5 features) is not ideal?
Yes if you're doing it manually via RDPing into the server. Because if for some reason your VM goes bad and Microsoft replaces that VM with another VM, your changes will be lost.
can you suggest of a way on how can I deploy a .NET 4.5 web application with .NET 3.5 feature dependency.
Do take a look at Startup Tasks
to install additional dependencies. They get executed when your role starts so you could enable the features (or do any software installs before the role starts). I haven't tried enabling the features personally (so I may be wrong) but take a look at this blog post which talks about installing these features through PowerShell or Command Line: http://blogs.msdn.com/b/sql_shep/archive/2012/08/01/windows-2012-and-net-3-5-feature-install.aspx