I'm sure like myself may people have wanted to use the small layout for the ship interiors either because they are flying a smaller ship or simply prefer the more logical and compact design. When I first started playing this the first thing I did when I could customize my first ship was to change the bridge and then change the layout to small. I was so excited because finally there was an interior layout for a Star Trek ship that made sense, and then....
I had to spend 3 weeks in sickbay because of all the bruises and trampled-on injuries I received from MY OWN crew simply because there is a hugely disproportional amount of crew wandering around the ship for a layout of it's size.
I talked to Tumerboy early this morning (3-30-12) when he was on and asked him to bring it up in the next meeting. With the interiors becoming more and more functional I really think more people will be switching to the smaller layouts. He said he would bring it up at the next meeting so this is as much a reminder to him as it is to let everyone that really likes the concept of the small layout know hopefully this will finally be getting looked at.
At it stands they are all the same, its the same sickbay, the same mess hall, same everything .... the difference is how long are the corridors.
Each design should fit the size, small size should mean a sickbay about the same size as we see in the Prometheus or the Defiant, medium size should be the one we see on Voyager and so on ... not stick a Galaxy-Class sized infirmary on everything.
As for the wandering crew ... this is I suspect caused by fact its spawning the exact same number on NPCs regardless of the map size and this is wrong, Voyager had a crew of 160 and 15 decks, meaning at best we should be seeing about 20 people wandering about on deck if we are using a medium sized deck.
The current system seems more of a placeholder that does not seem to be given much thought.