Currently I've got three things I'm thinking about re: pirates.
First, we're talking about battle population on a per-nation basis. That means that we could potentially give pirates a higher pop cap than other nations -- specifically, we've been discussing port battles, but I could imagine applying this concept elsewhere. We're still hashing out the implications of this for PvP, so we're not anywhere near making it happen yet.
Second, we're doing a complete tuning and balancing pass through the skills. You're absolutely right that the pirate skillset was constructed with solo effectiveness in mind, and that the Navy skillset was constructed to make them much more powerful in groups than solo. However, we don't intend for pirates to be unable to group, or not competitive in groups. There are a lot of skill tuning changes coming in 1.2 and 1.3, and we're looking at what pirates need to be competitive with their particular playstyle (which is to say, emphasizing maneuver and position over raw throw weight and armor). We'll have more to tell you about specific skill tuning in the very near future (which is to say, Taelorn is finishing up his initial pass through the skills even as I type this).
Third, we've got alternate port battles on the schedule, which really means 'pirate-specific port battles'. We want to create port battles that feel more like pirate raids and less like line battles. We're talking about alternate victory conditions, different population caps, and ship size restrictions on entry. These are fairly large chunks of work, so you won't see it in 1.2, but it's on the way.
Generally, I don't want to remove pirates from the conquest game; I want to make them effective in conquest in alternate ways. The ability for pirates to repeatedly raid minor ports for victory points is a small step in that direction; I'm looking for ways to systematically change the pirate conquest experience so that they can 'win' while feeling like they're pirates, not a navy with black sails. I have some thoughts on how I want to do that, but they are not set in stone yet -- which means I'm taking suggestions about pirate conquest mechanics. If you have an idea, let me know so I can potentially add it to the list of pirate feature enhancements I'm working from.
Also generally, any time you find yourself thinking 'devs hate pirates': you're wrong.
But you have a
way more hands-on experience of pirate gameplay, especially in groups and especially at higher levels, than most of us do. Even when we're playing, we're still thinking about the big picture, not the moment-to-moment experience. So the best thing you can do when you encounter something that's obviously stupid: let us know about it. In most cases, it's something we just don't see as a problem -- but if you do, then we need to take another look at it.