the Titan novel series explores that point, humans being a minority on the crew.
it's stated a big reason why the aliens tend toward the minority and humans the majority is largely due to problems in putting a number of vastly different races on ships together. like 3-ft tall aliens along side 6' humans having trouble reaching controls, big spider/crab type aliens having trouble walking down a corridor, water-breathers needing to wear special suits outside their quarters...
All problems with which I am both familiar and of which I can see easy remedies.
The simple solution is to create several parallel habitats which are slightly
different to accomodate a cluster of species. This might not be feasible in
a constellation size ship, but a galaxy class could be retrofitted with 4 or 6
sections in the saucer hull, esp if you drop the number of residents down from 3000 to 1000 or so.
Many of the fan created ships are significantly larger than a galaxy class
ship.
Yes there are problems, but Star fleet seems to get the IDIC principle,
and it wins against species such as the Borg Via the assorted differences
of thought of different species and perspectives. This is not merely theory
or good drama, it is simple systems theory fact. Any different species will have different neurological pathways and different brain structures, and will think in different ways. The combined intelligence of a group is fundamentally based on the diversity of that group. 2800 humans and 100
aliens on a Galaxy class ship is simply a dumb way to use the sentient resources of different species. I understand how and why star trek as entertainment was forced to cut corners, but the simple reality is that the larger the the diversity the smarter the group intelligence and thus the more powerful its problem solving skills.
For this reason, the factual reality of a star trek like civilization would be that they would mix it up as much as possible. Certainly it is true that some species would simply not go well together, either for psychological or ecological reasons, but it is just as true that in a galaxy with thousands of different sentient species haling from as many different worlds that there would be many species who would be likely to be comfortable or nearly so in Human standard ecological conditions.