I think at least part of the original script was set closer to the Kalahari region, which is where meerkats are from; otherwise it's just general geographic inconsistencies. That said, I think they could get away with species-swapping a few characters to make more geographical sense. For instance, making Timon some other type of social mongoose -- like a banded mongoose:
http://www.krugerpark.co.za/images/1-ba ... e-590a.jpg -- would be a great choice and wouldn't remove anything from his characterization. In fact, real-life banded mongoose are known to form close associations with both baboons and warthogs, so you already have a built-in ecological reason for Timon and Pumbaa to hang out together in that scenario. (And confer with Rafiki, if they want to hint at any of that
Lion King 1.5 dynamic.)
As for things they could do to more accurately represent the various characters design-wise, I'm sure they'll find ways to work around it. They'll probably just default to more realistic colors for various characters while still trying to keep the individualized designs, especially for the lions since there's so many of them to have to keep track of. This doesn't have to reduce the movie-accurateness of the designs of course; if you look to biology, there's ways to make it work. For instance, Mufasa and Simba can keep at least their golden pelts due to erythrism, a condition that makes animals more reddish:
while Scar can have more grey-brown tones (complete with mostly black mane) like so:
Rafiki could be made to be a proper baboon and it wouldn't change anything, he just wouldn't be naturally colorful, although they could have him paint his face as part of his ceremonial position as Royal Mjuzi if they're going to keep that angle. Same with Zazu; if they want to make him a proper hornbill species then it won't matter all that much that he's not bright blue.
At this point my greatest fear is that they'll try to pull an anthropomorphized look like what Andy Serkis' Jungle Book film
Mowgli is doing, but given what they did with
The Jungle Book, I think we should be fine:
https://www.youtube.com/watch?v=YzPUQsuHvEg