Well Fireshock, I agree with point 1 and 2. However, I do believe that you can add "Optional" structuring to combat and PvP. An example could be when quests are a thing, and you have NPC factions. Imagine the ability to "ally" your faction to an NPC faction. Givving you some benefits, but setting you at war with anyone that NPC faction is at war with. The NPCs could give out quests/missions to hunt down their enemies, or to help "Build" their defense ect.. Doing something like this, could allow for more structured PvP. BUT you would still have unstructured going on at the same time.
I think any tactic that is both low risk and high reward, is unbalanced. This would include the OP's version of torpedos with (imo) massive boosts to damage and blast area. I think these could be balanced to be "Medium Risk, Medium Reward".
An example of this that I am looking into (relating to warheads and torpedos) is to increase that overall damage output, but lowering the blast size. SO although it CAN blast through 2 layers of advanced armor, and hurt a handful of blocks (think like 5), its still not over powered. The idea is that its effective, but not so effective it can be exploited. SO a few torpedos to your hull isn't going to even come close to crippleing a well designed ship. MAYBE a smallish turret, but not a ship.
IF proper balancing is done, then all you have left are the asshats that go after fresh spawns. AND the guys that only want to attack people's stuff while they are offline. Those two things lie in the realm of server admins. Although Better tools are needed to aid in this area.
I want to be clear and say I do NOT think being a pirate and going after people is griefing. Doing it to the point that people are quitting the server IS. The only way to police this is with good, active admins, and good admin tools.
Anyway... just my rambling 2 cents.