Quoting: Zereth
Actually, he problaby shouldn't be able to. How are the companions without mecha getting around in deep space? Transporting people who don't have their own space-flight capable mecha _should_ be a benifit of having a spaceship.
True. Companions who don't have their own spaceworthy mecha should get left behind when the PC leaves town. But then, certain mecha should have passenger seats... that would then open up the problem of providing an interface to assign passenger seats to all the companions.
This still doesn't entirely solve the problem, though. If a PC has a lot of companions with mecha, he might find it more convenient to travel the world map on foot rather than dedicate enough cells to take everything. This is a bad thing- what's the point of having a ship if it's more convenient to go places without it?
There are two very easy ways I could solve this, but I don't like either of them. First, I could use the "Morrowind Horse" solution- companions never follow you when you explore the world map by yourself. Alternatively, I could use the "Cloud's Backpack" solution- any spaceship can hold as many NPCs and mecha as you want without dedicating cells to it. There can be a prop elevator somewhere labeled "To living quarters".
Here's another idea- always allow the PC's lancemates and their mecha to ride the ship, but require lodging cells for companions who are not currently members of the party. The advantage of this one is that it provides all the benefits of traveling on foot plus the convenience of having a spaceship. The bad part is that it could lead to some strange metagaming- when preparing to leave port, the PC might have to rearrange the party in order to take everyone he wants, then change back to his regular party roster at the destination.
Anticheese- that's a good idea. It'd be a lot more work, but it does have certain advantages. Certain cells, such as sick bay, could take up more than one cell by default.
Some new pictures of ship combat:

This one shows battle damage:

The meshes/textures need work. Everything is saved in Wavefront .obj format, so they can be easily edited in most 3D programs.