Well like I mention a lot in my forums post. The functionality of the Ship Interiors should be more like Star Trek Bridge Commander.
My ideas below are to just give a purpose to the interior of your ship, a reason to go here or here to get things done instead of just clicking on your UI to do everything. Gives your Star Trek universe a more realistic feel, but only if you choose to do in "Interior mode". Time consuming..maybe but that's what I want if I am going to have ship functionality.
1. Bridge: Well I would like to be able to just control the ship just like you can on your bridge on Bridge Commander, but that most likely will not happen,...so to be realistic in what cryptic can and would be willing to do lets just be able to view/send mail on one console and the map on the nav console, fleet, c-store etc. on other consoles/
2.Captains Waiting room: Contact Starfleet and adjust your BOFFS Skills with the reset option.
3.Sickbay: Like chris said on the last episode, buy hypo sprays and any other health related items.
4:Ten Forward/Lounge: If you like to use the food and drink items this is where you can buy theses things and also have a good social gathering, witch to add...is why I really want them to scale down the bridge size, so you can do your social stuff in Ten Foward/lounge.
5.Armory: Obvious to buy your weapons and shields/kits, maybe even allow you to make custom modifications to your weapons, like buy a scope for that sniper rifle you like to get a better shot from a greater distance. Also buy a better recoil to get a more rapid or single shots out of your weapon. The list of part can go on and on even get stuff to mod your personal shields.
6.Engineering: This is were you can "apply" (see #7 to see why i say "apply") your ship items and like the Armory idea I had make modifications with other parts to better your ship systems, and make it a better outcome to go towards that particular system if your a Tac/Eng./Sci officer. For example...If your character is a engineer then you can apply a even stronger performance to your shields with that "Shield Generator Enancer" you bought to make your shields stronger, same idea for engines. And of course if your a Tac Officer the idea applies to your weapons and Sci officer would be for your nav dish, buy batteries. This kind of take the place of crafting but maybe that can be done here also and remain a separate option. To add one more thing if you want to change the look of your ship then you have to dock with a starbase.
7.Cargo bay: This is where you "buy" your ship systems or pretty much just where the location of the exchange should be.
8.Transporter Room: Maybe a tuff one for Cryptic but this is where you Transport down to that planet or starbase etc. If in Range of course.
9.Science Lab: Maybe make this where crafting is done instead of engineering.