True enough. But as this condition, resulting from fairly routine operations rather than battle damage, eventually did force the evacuation of several decks, it wouldn't be too out of the line to speculate that the crew already had to avoid using certain functions and spaces when leaving port; having Main Bridge be one of these would then explain the use of this facility that seemed to lack classic things such as viewscreen or helm console.
As for the Prometheus, the plot has our very small and low-ranking band of heroes play a major role in running the ship. This would be consistent with a small bridge where the top officer wears Lt (jg) pips; the use of the Nebula class exterior is the inconsistent thing here.
We could always speculate that the ship did have a large and high-ranking crew appropriate for a Nebula, and that the absence of high-rankers was due to the authoritarian way the terraformer Seyetlik ran the ship; he himself may have held the rank of Captain, but would refuse to wear the uniform... And the only people with the guts to oppose him would indeed be doing so, off camera (just imagine the XO, of full Commander rank, lying stunned on a corridor just outside the shuttlebay, with the LtCmdr Second Officer hyposprayed to unconsciousness at the Sickbay right next to the CMO) while Sisko interacted with the Lieutenant on the bridge.
Perhaps the special terraforming mission and Seyetlik's antics also meant the regular crew was not given access to Main Bridge, the nerve center of Seyetlik's experiments, and had to conduct everyday operations from the secondary bridge?
Timo Saloniemi
