I just don't see the need for this. All it does is an add an extra step between 'Pregnancy' and 'Birth'.
There's also the point to consider that when reptiles breed in zoos more often than not the eggs are removed and placed in incubators to ensure more successful offspring. I have taken part in this process myself with regards to tuatara as part of the breeding programme.
So really, if you imagine that somewhere between the animal becoming pregnant and the young appearing in the habitat the eggs have been laid and removed, then the current system is reasonably sensible. Birds are a different story, as it really depends on the species as to how zoos deal with bird breeding, but quite often it's the same situation (this is also largely because wild pests such as mice and rats can get into birds' nests, even in aviaries, and ransack the eggs, which is pretty bad if your plan is to breed an endangered species).
I know that flamingos are usually hand-reared. As chicks puppets are often used to simulate parental care, so the chicks recognise the puppet as their mother rather than the keeper (which is of course helpful when the young is reintegrated into the flock). Peafowl on the other hand tend to be free-roaming rather than contained a lot of the time, and their breeding is often uncontrolled.
In any event, I don't think nest-building is a necessary or especially realistic (at least not in most cases) addition to the game.