Don't pay any attention to the nerds (Read: the people who are fixated on how wide the seats are on the Enterprise-E

).
Ooh! Ooh! I get to do some more divergin'!
True, fanfic writers can overthink the hero ship just as much as or even more than the individual characters, but there can be at least one benefit to having a clear picture of how a ship looks and how it's supposed to function: if you make it robust enough, stupid technobabble shit doesn't happen.
F'rinstance, the Enterprise in my AU Trek series was created according to a principle I call Matt Jefferies' Original Intent, which is essentially how Matt Jefferies said the original Enterprise was supposed to work before other creators wrote their stories and ended up evolving starships into what's canon today. As such, MyWayPrise doesn't have an engine room, is mostly featureless on the outside, most of the living and working space is in the saucer, and the secondary hull is mostly for storage, while the warp engines operate independently of each other and are the things you dump in the event of a problem, instead of separating the saucer. I keep all this in mind when I'm writing those stories.
Why bother? Focus. Out of all the story ideas I came up with for the series, not one revolves around some technobabble particle snaking into a Bussard Collector or a vent somewhere and causing a technobabble malfunction, because I
know my ship doesn't operate in a way that that can happen.
My point is, if the goal is to write character driven stories, then they
can't be about the ship the characters are on, but that's exactly what you make the story about with one of these technobabble malfunctions, something even canon writers couldn't keep themselves from doing (across all the series, though TNG made it an art form). Of course, there are plenty of ways to avoid this in stories, but the way I've found works great: simply know what your ship can and can't do and what can and can't happen to it so that you won't be tempted to write a story where some frinxabibble particles infiltrate through the ramistat manifold and cause a matter/antimatter infarction in the core that shuts down the Einstein/Rosen coil in the holodeck driver matrix and makes the ship have a baby, 'cause as soon as you form that thought the little Engineering Continuity voice in your brain will say, "Wait a second...that shit can't happen."
Seriously, though...the seats on the
Ent-E could be a little wider.

Just sayin'...