To offer a counter-point to humanocentric ships: different species have different environmental preferences and needs. We know Vulcans are used to warmer temperatures and higher gravity; Andorians thrive in cold environments, Tellarites (from what little I recall) gravitate towards swamps and bogs.
It seems pragmatic to have ships favor a species on account of not having to maintain several layers of environmental settings, some of which might be opposed if not outright incompatible. A ship full of Benzites would have an atmosphere that does not necessitate wearing the breathing apparatus we see Mendon wear; a ship full of Elaysians may be able to run minimal artificial gravity, etc.
No love for Picard reciting a sonnet in TNG: "Ménage à Troi"? :) Or were you just specifically listing references to Shakespeare plays?