At the moment, having an animal companion out and doing anything other than killing or chatting, is cumbersome to the extreme. It's basically like giving all creatures of the Underdark bar rothe permanent true seeing, since at any given point, they will undoubtedly see that rothe/bug/bat/other normally seen creature of the Underdark wilderness, and happilly charge it at full force, just because it happens to be bonded to a player. This is because of two reasons; They cannot stealth, and they share faction with their master.
Now, somehow enabling your companion to stealth would be a solution to this. It would, however, be a very unsatisfactory solution, as it would basically only help the animal companions with naturally high sneaking skills (Prowler, Bat, Rat), and not the other ones.
To help fix this, I would really love to see a faction change of animal companions. I am not at all sure if it is possible, but to let them share faction with their non-companion, wild counterparts, would go great lengths to solving this rather sad problem. Rothe companions should not be attacked by every single creature out there, but rather only by predators such as Hunting Spiders, Prowlers, and the other creatures that currently attack wild Rothe. Deep Hound companions shouldn't be jumped by their brothers every time they meet. And so on.
Adding stealth, and proper factions, to animal companions would be really awesome, and once and for all shine the light deserved on what is supposed to be one of the major perks of druids/rangers, a perk that is currently limited to being used during roleplaying sessions in the first section of Underdark: East, instead of following their master wherever he goes, as it should be.
This also would not be overpowered in any way, as powergamers can just summon their companion when needed, anyway. The only thing this does, engine-wise, is to add the risk of enemies spotting your animal companion, in addition to yourself.
As I said, I do not know if either suggestion is possible to fulfil, but if they are, I cannot think of any reason to not do it.