And with the release cycle on VS & MVC being as it is you have to redo them every year.
And I start maybe 4 projects a year... Really, really not worth it. Ofc, excluding the 150 console apps I make a year.
They only thing I do actually do is switch the console apps from client profile back to the full framework, that was another strange decision given how most people use console apps to test snippets of code due to the lack of a REPL.
In practical terms you learn to stop mucking around and just live with the defaults if you use a lot of different machines.
That said, I'm sorry you had a bad experience. For most, you'll want to File | New Empty, then:
install-package jquery install-package modernier install-package angularjs
I disagree with your frustration about deleting references. You hit delete a few times or uninstall packages and the move on.
BTW: ScriptCS is a nice REPL to check out: http://www.hanselman.com/blog/ProjectlessScriptedCWithScript...