With a simple .vim, your Vim configuration is a living, breathing thing, and you can easily modify any script you're using the moment you find a bug in it that interrupts your work: You own your vimfiles. When you manually upgrade a script, it's trivial to roll back to the last version that worked. I guess dotfiles are the last place I want to introduce needless indirection: They should represent my work environment at a point in time, precisely.
I can only see two benefits: The ability to try out new plugins quickly, and the ability to upgrade all of your plugins at once quickly. Are these worth sacrificing control over your editor config? This has puzzled me since the day tpope released Pathogen to much fanfare.