Assuming Cryptic does come back to Fed ships and re-does the interiors to bring them in line with the rather nice Romulan designs (get that engine room!), what but would you like to see redone or added? Few things I've been fancying recently are;
Multiple cannon engine room designs like the bridges (TNG engineering is sooo nice, and it would be good to see the Ent-E engineering in full original glory)
Larger sickbays? - not sure how the one we have is meant to serve a ship of over a thousand?
Stellar Cartography (don't tell me that wouldn't be beautiful?)
Editable captain's quarters
Things only referenced on the show, or in technical manuals like large recreational areas, hydroponics, or the arboretum.
They need to fade the captain into the bridge, not beam him in and out. If he's beaming in and out, where does he beam from/to? It's weird. Just fade him in, or wait to show the bridge after the captain loads.
Also, make the Fed bridge officers actually sit in, not hover over their chairs. The Romulans can do it right, why not the Feds?