IMO, using animals in combat in games doesn't usually come off well.
For one thing, I suppose I have an ethical problem with sending an animal, who can't voluntarily decide to join my squad in the same way that the other companions can, into a situation where it can be injured or killed. I know the obvious retort will be "then don't pick the animal as a squadmate," but that means I have to miss out on any content specific to the animal.
The other problem is that dogs - which are the only animals I've ever seen offered as companions in games - are not realistically going to stand much chance against the kinds of enemies we typically encounter unless you make them ridiculously overpowered.
I like having pets around in games depending on the circumstance, but when they do turn up, I always end up minimizing their role in combat. I almost always left my dogs in DA:O and DA2 at camp and Hawke's house, respectively, only taking them along when exploring cities or otherwise doing primarily non-combat missions. Dogmeat in FO3 stays at my Megaton house, again coming along only in non-combat areas, and Rex in FO:NV gets returned to the King once I've finished his mission.