Some Star Trek books took the opportunity to work multiple species into the Enterprise's roster, when you don't have special effects problems with doing so.

But some others took the approach that Starfleet has a lot of vessels, and they're still somewhat segregated by species just because of those issues, and while the TV series don't corroborate that very well, I think it's better fanon overall. Peace and harmony among the species is great and all but trying to work 17 hour shifts in 2.5 Gs is going to get really old for the humans. And who wants to wear complicated breathing apparatuses for years at a time?

It would be an interesting direction to take a book series in... why do we see so much about the Klingons and Cardassians and Vulcans on TV? It's not because they're the only important species, it's because they're the species that breath our atmosphere at more-or-less our gravity and solar cycles. The Federation could be a whole bunch of parallel Federations-within-a-Federation where there's an entire set of species who also crew with each other but breath methane, need .7G, and work around 14-hour day/night cycles, and they just don't interact much with each other, not because they hate each other but just because it's so tedious to have prolonged contact.