Hi GP and welcome to the Cafe.
I don't think you played the game well enough, otherwise you'd know that a lot of what you are proposing is already in the game. Other things are usually there or not there for a good reason.
1. Pirate should have money to hire labors to work on the island. Those workers should also have right to use the island facilities such as restaurants and relaxes.
Aw, how boring. Why hire workers and pay them, when you can kidnap them and make them slave?! Are they pirates or lilly-livered Dutch merchants?
2. Pirate ships should have ability to command as a fleet to loot settlements. An encounter message should pop up to player about what kind of ship the pirate confronted then player can decide to engage the action or not.
You can raid settlements for captives and your ships do operate as a fleet if you send a couple of them to the same seazone. As far as messages and commanding ships goes, sorry there was no radio in the 17th century, so when a ship left the harbor, people on shore had no information about it until it returned. This is quite accurately modelled in the game.
3. The pirate should be able to occupy the settlement as supply post, it might not be for immigrants but just a remark for pirates. The other 3 nations can take back the settlement later.
Well, seeing how long-term occupation has never happened in history, I think it's reasonable that you're not allowed to do that in the game. Besides, the game revolves around your island, and things like this would be a bit out of the game's scope.
5. Pirates are not just confronting engl, fran, spai ships they also will meet the other pirate ships.
And pirate ships are one usually one tough nut, too.
6. Pirates should have other things to do on land not just eating and wenching.
Well, they also drink, gamble, sleep, stash away their gold, pick fights with each other and kill captives. It's hard enough taking care of those actions.
7. Whenever calling the set sail bell, all pirates should go on board immediately. Sleep is not important in every game.
Hehe. It would be nice, wouldn't it. It'd be even nicer if no pirates were ever killed and always brought you tons of loot, guaranteed. Unfortunately, it's not all that simple.
9. The winning victory should also depends on how big area you own the sea.
Well, this is pretty much the same as the number of ships. The more ships you have, the more seas you can control.