There are a lot of gameplay discussions here, but not much reference to history outside of Fluffy_Fishy's posts. I can't help, unfortunately, as I know little about naval history in any period. But IMO the first question in EU should be "What are we trying to model?" rather than "What system is interesting?" EU is fun because of the ways the various models in the game intersect naturally with one another, not because it's engineered for "fun gameplay". That kind of engineering is why I gave up on Civ.
Any implementation of "Sailors" similar to what we have now is a limiting factor, just as manpower limits army recruitment. So, historically, what were the limiting factors on nations fielding strong navies? Did countries ever "run out of sailors"? I don't have historical evidence at hand, but maybe Fluffy or others can elaborate. My impression is that filling boats with people was not the issue - as noted above, most of the men on a ship were a rough lot, sometimes pressed into service. Certainly the raw cost in materials and time to build ships mattered, and we've got that in the game already. But officer quality may well have been a factor too, not in the sense of individually brilliant admirals with tactical insights, but in having a small cadre of well-trained officers to handle the more skilled tasks on ships. That might be modeled with a system somewhat like Naval Tradition, with a point value that increases over time as your navy gains experience and less skilled sailors develop into more skilled veterans. That value might limit the maximum number of ships that can operate at full strength - beyond that, a sovereign might build ships but lack skilled officers to command them, incurring a combat/trade penalty. But again, I don't know the history here. Maybe personnel really wasn't the issue compared to the material investment of building the ships themselves. In that case, just drop the idea entirely and make it purely about money and time.