"Crappy implementation"? If you're friendly with the animals and asbolutely everything else is hostile to them already, how would YOU break down the faction reaction? What the second rank did in Fallout 3 was make you a protected member of the animals faction. If you came under fire and there was an animal in the same cell as you, the animal came to your aid rather than just attacking mututal hostiles within their detection range.
Which was very often a distinction without a difference. Not always, but very often.
How would I have handled it? Using something similar to Robotics Expert, where the second rank let you interact with animals, in this case not to deactivate them but to get one to follow you until you selected another animal. Then you wouldn't have to retreat towards animals you'd seen 30 seconds ago to feel the effects from the investment of 2 perks + 5 largely useless points of Charisma.
In F:NV, Charisma apparently has greater value due to Nerve, so the 5 points of Charisma aren't as wasted as they were in FO3. But, again, 2 level 10+ perks out of a total of 15 perks, spent on the same effect, should make a strong difference. x2 Toughness saves you 6 health every time you get hit, and those start being available at level 6 and have 1 point lower stat requirement + no skill requirement.