1) The kind who investigated the goings-on in the ship, interviewed the officers and chiefs, and learned how the ship was being run, then made small changes over time to optimize the operations based on what they learned. Sometimes big changes in one specific area, if it was required (like fixing the ship's crypto key material protocols, if they are super fucked up).
2) The kind who came in and ran roughshod over the whole ship, made a bunch of big changes and policy decisions, and generally acted like they owned the place in order to fulfill a pre-concieved vision they had of how things should be.
With 1, we were happy because there are always improvements to an org, but the best people to know those improvements are those who know the org. These commanders always resulted in a better command overall by the end of their tenure, bar none.
With 2, we were sad, because suddenly mistakes were being made everywhere in order to try and fit into the "vision", and thus reduced morale due to the massive changes and the constant failures. I saw 2 of these and both failed miserably and brought the command down lower than it should/could have been. One of those was on a great ship that performed so flawlessly that we were always sent on the most important assignments, and after I left I learned the ship fell into disrepair and could no longer even get underway, due to mismanagement. That guy came in and basically made me decide to get an early re-assignment and 3 of my friends on that ship left the Navy completely because of him.