If you could keep the exterior exactly the same, which parts of the interior would you change or leave out? I'm writing up a new version of the NX class for my take on Broken Bow, leaving the exterior, but the interior's up for grabs. I was thinking of moving the warp reactor to the warp controller area of the ship, out of the saucer section. Good for ejection in emergency, bad to get hit in a fight. The transporter is out, but what could I put in its place there? Perhaps a real movie theater?
That's a pretty big space, but you don't have to replace it with another large room. It could be subdivided into some of or a mixture of these: Short corridor. Crew quarters. Science lab. Storage room. Auxiliary Technobabble Access. Or even a dog park. Edit: I'm assuming you meant the engine room, but then you say the transporter is out. So you want to replace that alcove it sits in?
Actually the interior of the ship is one of the things I think Enterprise did right. The bridge was a standard bridge with a few kickbacks to the TOS era of time. The quarters, and hallways and such were crowded and functional as they should be. The engine room was a nice take, it was actually kinda scary looking that giant hulking thing in the middle that apparently made it go. It was a nice ship from the inside.
I remember reading that the interior of the ship was supposed to be cramped and very close-quarters, like a submarine. However, I never once felt the ship was at all like that. If it had been, it would probably have felt more realistic as a "primitive" space vessel (to use Spock's words).
I liked the aesthetic of most of the ship for sure, and the deckplans I saw here, and here, I'm going to try to follow best I can while writing. I thought it was functional and a reasonable leap from NASA to humanity's first deep space ship. It looks like C-deck has a nice observation housing for seeing things pass by in space. I might use that in my first story. I'm going to pass on the 'command center' since there's no Xindi to necessitate getting rid of cargo space for it. Besides, there appear to be plenty of other rooms that serve the same purpose. Any other rooms you'd change or highlight specifically that didn't get enough screen time in your eyes? And do we even need the saucer impulse engines since we have the main impulse engines also?
Bringing the warpcore all the way back to the section between the pontoons (spelling??) seems like a bad idea. Like to you said, easy target. But also difficult to reach for maintanance and such. For somebody who used to work with cars a little bit, I can tell you, you want the engine to have easy acces. The way it was done in ENT makes sense. Sure, it can seem dangerous. But nuclear subs have their powercores in the ship, right? Not dangling out back. As for the transporter.... I say keep it, but use it like it was supposed to. Approved for bio-matter, but people being dead scared of it. They got used to it way to fast IMO.
Get rid of directed energy weapons (other than small point defense ones) and add more torpedo tubes (which can fire scientific probes of the same diameter as the weapons). 10 or so along the bow; 2 dorsal and 2 ventral pointing forward; 2 aft. That's 16. Tubes are nothing special. Make them all automatic/robotic controlled. Magazines can be protected and deep in the ship; the torpedoes we see are fairly small, so they can carry lots of them. Add more armor plating; enough so many of the "alien of the week" direct energy weapons can't breach the hull. Needs a bigger medical bay and more medical personnel. Shuttles can have hardpoints to externally fit the torpedoes the ship fires/specifically designed munitions for various tasks. Allow shuttles to dock externally so that they can carry more if need be (recessed area of the hull that can piggyback five shuttles or so). An aft minelayer (much bigger diameter than the torpedo tubes). Large yield proximity/magnetic devices for use against cloaked Romulan vessels and highly agile Klingon Birds of Prey. Probably don't carry the mines on normal expeditions due to safety concerns. That'll pretty much contend with most of the military threats they encounter until they get to the tech level as seen in USS Defiant from In a Mirror, Darkly. Don't mistake these increases in combat effectiveness measures as pushing it more towards a military mindset -- they're just tools that the crew can use when they're attacked (and they always seem to be). A military mindset comes from the actions, not the items. Try and get the Vulcans to give up their improved tech in regards to scientific exploration. Adapt that to the ship. Keep on working the transporter and the theory behind it. The more they use it, the more experience and insight into the things that can go wrong (if you don't use it, you don't know what is unforeseen). That's what I'd do to the NX-class to begin with. Its speed seems to be fine, really.
Id get rid of that wide open area at the back of the bridge, which opens it up far too much. See the USS Kelvin bridge for how effective and primative-seeming a more cramped control room can be. That back part of the bridge also gives the unfortunate impression that the Enterprise bridge is a minor redress of DS9's Defiant, which had an idential area with with an identical table at the rear.
Rid the ship of the elevator, replace it with stairs. Private living quarters only for the Captain, First Officer and Chief Engineer. Junior officers should at least double up and most of the crew be in bunk rooms. Put a big thick armored door that swings closed in front of the regular inner doors to the air locks. Something with a manual latch, it's way to easy to board that ship simply by docking with it. I'd make the majority of the corridors narrower.
I'd do away with the conveniently heavily-shielded walkway in the nacelles. Include science labs (it is an exploratory craft after all). Externally I'd have a separate drive section (where the deflector dish would be located), thus making the front of the saucer round.