Ship and Weapon changes

You make some good points. Weapons in general do need to be rebalanced.

I like your suggestion to make missiles use shields instead of hull. It would be cool to have to select what you want your point defense to be good at shooting down. I don't agree that the point defense need to be buffed though. Many variants can be quite good at shooting down missiles and they do a ton of damage at close range. If anything they need a way to be more effective against missiles without doing so much damage to larger ships at close range. Point defense currently also force you to think about positioning if you want to be good at shooting down incoming missiles. However, this ends up penalizing movement, which is probably another point in favor of buffing mobility.

I think the best way to change mobility would be to add speed and agility modules for blue slots that work as a percentage of the base hull stats. That way the smaller ships will always be faster than large ships. Like you said, it would be best if the larger ships were more powerful (more weapons/health) but not better in every way. If the modules provide a flat upgrade, you could make even the big ships fast, which would be bad. It would be really cool if you could choose between small fast ships, and barely mobile capitals, or even a mixture that you could direct independently. Encouraging and enabling multiple play styles is super important for replayability.