I like the idea of capping claims per character, however my concern is the resource factor if every flag claim had a building, shipyard and all that jazz on it. Islands would not be very sustainable. So perhaps keep it lowish for solo players (3 or so) and tribes maybe get a bonus claim for x amount of people in the tribe (more people means more space needed).
The claiming and contesting needs to be looked at. You could make it like the lawless area buildings....decay in 4 days if you don't go on it, then if it doesn't get refreshed by the player the claim vanishes becoming free. That way all the claim spams will go because those people are not going to be sailing everyday to all of their points.
Though that does run into the issue of say if people lose their internet connection and can't get on to refresh, or holidays..hospital stays (unfortunate life stuff getting in the way), it would make it a little unfair so you could add in a feature to select one flag as a main base, to allow more time on that one or if someone sleeps on it, it can't be claimed for a longer time.
You could even add in some more Islands on the map too, there is plenty of room for that.