Part 1:
Definitely not include fully marine animals - including the Manatee ya'll.
Part 2:
I'd like to say include flying birds but this is about the Habitats, not walkthrough/non walkthrough exhibits. Flight's only been shown in walkthrough exhibits, so as such they shouldn't be included in a habitat list. I also feel that they'd skew the numbers very heavily in terms of what people want - quite a number of players could potential put half or more of their list in as flying birds - myself included.
As such, I think the birds that should be included are birds that would generally work as non-flying in game, even if it's possible for them to fly in real life. The birds that could be included spend enough time on the ground in real life, that them being solely on the ground in game would not appear too odd. The wading and running birds for instance - Herons, Storks, Secretary Bird, Ibises, Roadrunners, Turkeys,
Additionally birds that spend a fair amount of time on the surface of water in real life could be included - Ducks, Swans, even Pelicans.
I think asking for Eagles, Owls, Toucans, Macaws, Cockatoos and similar birds may be unrealistic at this point. And I'm saying that as my ultimate no rules animal I want in the game is the Bald Eagle, and immediately after that comes at least one Macaw and Toucan - all this before the Wolverine which is my most wanted habitat animal at this time. I'm giving up that dream of having exhibit birds, though those could have their own thread again.
Part 3:
How small habitat animals could be - I know this won't be popular but I feel the Tamarin is too small for a habitat, but not by much. anything with a bigger footprint than that could be habitat animals - for reference Meerkats are roughly twice the size and weight of a Tamarin, based on information from Wikipedia (take that with not full assurity since we know wikipedia can be incorrect on things)
Part 4: I think the current setup and grouping is fine as it is, no need to change it.