There is one type of user that pays the startup cost of the system over and over and over again. It is YOU!
The developer is the one that keeps restarting the application, and overly long startup procedure will directly effect the way developers will work with the application.
Not only that, but since startup times can get ridiculous quickly, developers start working around the system to be able to avoid paying the startup costs. I have seen a system that had ~3 minutes startup time. And the developers has moved a lot of the actual application logic outside the system (XML files, mostly) in order to avoid having to start the system.
This is something that you should keep in mind when you trade off overall performance for startup performance. It is usually preferable to either do things in the background, or softly page things in, as demands require it.
This is usually something that require a more complex solution, though.