I like the way you've set up the matter collection system.
Honestly, Fred. You're very detailed, and I don't have many supplimental ideas. I would, however, like to draw a few similarities between the ship you're making and the ship I'm sitting on. You seem to have a fair understanding of the basic gist, so;
Pretend that space is water.
The seachest/matter collection assembly draws this water in.
The boiler/matter reprocessing unit makes it usable.
And then what? One massive problem I see that's going to either have to be handwaved or explained is exactly HOW the Matter reprocess magidget works. Does it have nanomachines roaming around inside of it that put particles together and conveniantly drops them off somewhere? Are there beehive-like catacomb-tube things that the matter is sort of electromagnetically drawn into, and then converted and seperated before it's even turned into useable matter?
Also keep in mind that these storage tanks - and that's what they are, storage tanks - are going to have to be large enough to keep the ship running for a goodly amount of time should the matter collection assembly fail. Anything less is poor engineering and planning - and tanks that large are going to end up taking up considerable amounts of space. You said that this assembly was three decks high.
Yea, I can see that sort of size. It might be interesting to describe all the pumps and various subsystems that would have to go into something so catch-all. Hell, I might even throw in some edits on the page if I can carve the time out to sit down and actually put something together. There's got to be plenty of mechanical pumps, macerators, and so on that go into the inner workings.
Macerators.
I'm not sure if there's a correct way to spell that. Regardless, that's what this is missing; what happens when something solid gets pulled into the intake? Does it get jumbled around for a little while, while the electromagnetic nets nibble it down to size? How are large particles broken up by the matter collection assembly?
It also seems to me that with these additions - the armor bay, and everything - you've promoted a frigate to a cruiser, in EVE terms. (I have been playing too much EVE lately). What I mean is, it's an entirely different ship class. Much larger, so the engines can compensate for the power demand. I don't remember you putting it into text, but there's certainly a lot more room for capacitors and energy solution subsystems.
The armor bay.
That's a damn good idea. I would like to suggest, however, that in the interests of saving space, the armors be stored on racks beneath the deck, as opposed to in containers. That way the armors could just be placed mechanically on the elevator platform, as opposed to... like... moving boxes. I may have simply misunderstood the text here. I probably did. Yep. Oh well, good idea anyway. You could also do weapons loadouts the same way.
Sometimes I think of donning power armor like donning firefighting equipment; there's just no good way to do it, unless you pre-stage. What if there were some way to, standing on the platform, have the armor - already open - just slide up around your legs. That way all you would have to do would be to close the chestpeice, coat-like, and grab the helmet? I'm not sure how to accomplish this but I am sure that coupled with the elevator it could save a great deal of time. Perhaps inertial systems would be required or utilized in some manner, as opposed to a physical elevator?
