Just to add my 5 cents worth...

Misenum only grew up as a naval base with the advent of Octavians war against Sextus Pompey. Lacking a proper naval base in the Tyrrhenian Sea Octavian sent Agrippa to Misenum to train a fleet. By connecting two inland lakes Agrippa was able to train without Pompey interrupting and bringing on a battle. Eventually a canal was built to connect the harbour and lakes, forming the first Roman naval base on Italy's Western coast.

Prior to Pompey's campaign against the pirates the navy was very much neglected by the Roman senate in favour of the army. When a fleet was required it could be obtained from allies such as Rhodes. Obviously the Romani had a fleet, but it wasn't powerful.

At the time of the social war (91-88bc) I thought the roman fleet was based in Ostia and some campanian towns such as Herculeaneum.

I have no idea where the main fleet-building infrastructure was located pre-principate, but I didn't think it was Misenum, (ie. I thought it was at Ostia).

Please correct me if I'm way off.