I prefer the newer version as well. Layout is definitely better, and I like the color scheme... however:
In both versions, you have a total of 19 seats (16 staff, 3 command), which feels a bit overkill for a "mid-size" Attack Cruiser like the Prometheus Class. Personal preference, would be a reduction of the blocks of 3 seats, down to 2 giving it a total of 15 seats. Still a considerable amount, but far more sensible in my humble opinion.
Of course, this is your design, and I love it just the same. Just throwing the idea out there
One thing currently missing though, is some sort of console for the First Officer to interact with.
Had another thought to add some visually interesting objects to the scene: A small, lit inset wall-shelf below the Main Computer display, perhaps for ship models of past ships of the same name? Alternatively, replacing the wall panels you currently have on the sides of the display, for ship-model display cases.
Dunno if this might clutter things too much, but would look nice 😁
Current location of the replicator, would probably benefit by having a smaller display screen instead, with the main screen being on the big wall between the doors. In keeping with what was shown in early TNG, will this table have built-in holo projection capability? Loved that feature in TNG, but didn't really appear again in later episodes/shows.
The Strange New Worlds version of the ship has had some alterations. Most notably on the external, the aforementioned windows. The ones immediately in front are likely the height from floor to ceiling. But the saucer of the "TOS Connie" has mostly been considered to be 2 decks tall in most iterations, so I'd say they look pretty reasonably scaled.
Another notable change, is the way the bridge looks. Warmer colors, new display graphics, and the removal of the "outer corridor" around the bridge, as shown in Discovery. Also a new secondary turbolift on the starboard side, near Spock's station.