This also works:

Sail full-speed into the Man of War without firing at it. When you get close and it starts to veer to avoid collision, let go of the wheel and charge up the center of your ship. If you are disengaged from the wheel and the Man of War hits you, it will not initiate a naval battle. Essentially, run as far up the front of your ship as you can, before attempting to launch yourself onto the Man of War.

I suppose this method is a bit theatrical, but man is it fun. Clear the ship through hand to hand combat, it's much easier than early naval wars with these galleons. When you get to the captain, bear in mind that your attempts to disarm and knock him back will initiate his counterattacks. Once the ship is cleared, go back to the Jack Daw, and fire once upon the vessel. It will go from full health to nearly zero, and will be boardable. Problem solved.

Warcraft 3. Dated to the pre-World of Warcraft era, this RTS was particularly known for its RPG elements, so much so in fact, that they based the entire MMORPG on this one aspect of the original Warcrafts. Factions have heroes, which can buy or trade equipment at vendors, as well as level. The fan base for the original Warcrafts is particularly strong, indicating that a Warcraft 4 on current gen graphics would do quite well.

Company of Heroes. This RTS hit the market with a big impact, and is made by Relic Entertainment, the same guys responsible for Dawn of War. Although released in 2006, it is still a graphically beautiful game. It features fully destructible environments, and tactical elements (such as infantry advancing behind tanks for cover, or diving into craters from earlier explosions). The units are upgradable with new weapon types, and can also pick up other weapons left about the battlefield.

The Battle for Middle Earth: This RTS focused on the War of the Ring that took place during the Lord of the Rings trilogy. This RTS might not have all of the unit customization that you're looking for, but it does offer this RPG aspect to its heroes. Heroes level up and learn new abilities as they grow stronger. With some heroes, they even have multiple sets of weapons that they can use, such as bow/sword combos.

Yeah...Starcraft is mainstream RTS. It capitalizes on combat tactics and not much else.

Stronghold is definitely worth a look: Strongold 1 and Crusader were great. Unfortunately, they keep seeing worse and worse additions to the franchise. Stronghold focuses on castles in the Middle Ages. There is an emphasis on some warfare, but it largely focuses on castle life. Also, it has by far the best base-building mechanics of any game I've ever played. You construct your towers and walls and station your troops on top of them to fend off enemy siege towers and ladders during sieges.

Age of Empires is good. Have you checked out the Online edition of the game? Age of Empires Online doesn't quite live up to the graphics of Age of Empires III or even the ingenuity of Age of Kings, but it's still a free to play RTS game that specializes in multiplayer. You have a home city that you build yourself, upgrade your units with equipment and research, and create a unique and diverse playing experience through a series of mission that span across the Mediterranean. 

Company of Heroes, as someone said, is the most beautiful of the RTS's right now. It makes use of a cover system like Dawn of War did. Environments are totally destructible, so the tank that your riflemen were hiding behind can be completely blown to pieces, and your riflemen could still use that tank's smoldering frame for cover for pretty much the duration of the game. It's very realistic, but if I can tell anything from your likes and tastes, you're going to be more into the medieval RTS's.

I'd say that Stronghold is probably the game you'll like the most. There will be another Stronghold game, and the studios that makes it won't be pressed for a release date this time, so it should be much better. What's more, it's Crusader 2, and Stronghold Crusader was incredibly addictive and still is. If they took Crusader and slapped new-age graphics on it, I'd buy it in a second.