I have some beef with the wildlife in skyrim just as a wildlife nerd and I think it should be corrected for future games. I think the universal logical nature of ecosystems needs to be respected.
For instance in skyrim there are way way way too many wolves, it doesn't make sense that there would be more wolves than deer (or even close). There should be about 200 deer for every wolf at least. Generally about 500 prey animals for every predator.
I like how there are assorted cervid (deer) type animals, but it would be nice if they differed in behaviour. There is a caribou looking deer in the game (can't remember if it's called deer or elk or what) it would be cool if they ran in big herds of about 20 plus animals flocking like birds. Then have another deer type that lives in groups with a stag and a few females, then have big solitary moose like deer or something like that which are perhaps liable to attack the player.
Predators should be slightly more likely to flee really. It would be cool if wolves generally fled but perhaps targetted the player when they were in larger groups and maybe be very likely to attack if the player is injured, or small in stature. They should also use hit and run tactics to weaken you gradually, using their quickness to dart in and bite and dart out.
It's kind of ridiculous how willingly they run in for their certain death over and over again, natural selection would have steered them away from that behaviour by now. You could have like suicidal guard dogs that are just balls to the wall aggressive, but wild animals should be more wary.
Ofcourse wildlife needs to pose a hazard for it to be interesting but it could be balanced better. In real life herbivores are usually more dangerous and aggressive, this could be incorporated. Bears should still be quite aggressive, but also more deadly and durable.
With cat like predators they should be quite stealthy, you should be unlikely to see them before it's too late and you're engaged in a life or death struggle after they have ambushed you. Ofcourse stealthy players could sneak up on them with skill, but it would be quite a feat. Really big cats should kill you pretty fast after ambushing you, encouraging you to be very very careful in their country (and it should be known by the towns people where big cat country is).
That's all I can think of for now, what are your beefs and suggestions for wildlife in the future?