Almost all lens will benefit by stopping them down a bit and it sounds like you have found the sweet spot on yours.
I do not have a D5000, I have a D80, but I would think you could set it up the same way. I use aperture priority and auto ISO with limits. Mine is set to default to ISO 100 but will increase as needed up to ISO 400.
You could also select an ISO without having it on Auto ISO and only the shutter speed would change.
Jerry Jaynes Great Smoky Mountains of North Carolina