@nimbleorchid1
A Navy doesn't work in the Sea of Thieves - the Devil's Shroud keeps them out, and many of them don't even know where it is, if they believe that it exists at all. The entrance through the gap in the Shroud is also too small and dangerous for fleets or even individual larger ships. The many shipwrecks scattered throughout the Sea of Thieves are the result of one such attempt by the Grand Maritime Union, the only group that wants to get in. They're currently trying to get through with the use of their shroudbreaking Ancient Coins, but we'll have to wait to see how that goes. Given how the last major invasion, being the skeleton armada, ended, I doubt it will be successful, as only pirates respawn through the Ferry and the battles of the skeleton fleet lasted for over a month straight, still continuing today.
For gameplay, a large navy still doesn't work. The skeleton armada was tailored by Rare to fulfill all of the requests - fortress islands with vaults of treasure; passive roaming ships laden with treasure; fleet battles in open sea and among larger rock formations; pirate-hunting ambush ships; etc. A navy can't do much of anything the skeletons haven't or can't, excluding maybe swimming.
For the new faction, buying direct advantages with in-game or real currency is not something that will be coming to the game. It goes directly against the horizontal progression that the game has, where everyone is equal in equipment and differs only in skill and experience. Also, trajectory lines for cannons would be incredibly overpowered.
For the 'top 3 crews' thing, I don't think that's a good idea, either. The game isn't meant to be played by focusing on grinding the most, it's meant to have you gradually gain reputation and gold in the background while experiencing the myriad of things to do. Giving extra to the top grinders incentivizes the opposite of that intended playstyle.
For taking sections of the map, that's one of the worst ideas on this post. This is not a game where you fight in a war in every aspect, it's a game where you are one of many pirates who are free to do as they wish within the area, provided the other pirates and creatures aren't able to stop you.
Customization for harpoons, and much more, is needed. There are so many smaller parts of the ships that could be changed - the railing, the rigging, the lanterns and compass, the bowsprit, the decorations on the sides of the hull (the current galleon having those decorative doors, for instance), the crow's nest, etc.