At the risk of sounding whiny about it, I agree. I don't think it necessarily always puts you at a disadvantage when the enemy is using it and you're not, but it definitely does at times. Yeah, this was in due to me not aiming my shots very well for maximum damage, I suppose, but there have been a few instances where I run up on a guy with his back turned to me, I start shooting him, his auto armor activates, he spins around, and kills me pretty damn fast. Of course, I didn't activate my armor, which I suppose I should, but I kind of figure if I'm shooting a guy continuously in the back without him initially knowing I'm behind them, I should have a good chance at killing him before he spins around. Not always so with auto armor. And it's happened enough times for me to take note of it. I definitely don't always lose a fight when going against someone with auto armor (and I never use it), but there are plenty of fights I've been in that I'm pretty sure I would have won if the enemy had to have activated his armor manually, rather than automatically.
I like the rank limit idea, but I highly, highly doubt that'll happen.
I feel like at this point I'm whining about it, but I do feel that it was a mistake to put in the game, and I know a lot of people have said the same when the Beta was out. Guess it's just one of those frustrating things we'll have to put up with to enjoy the game. Pretty much any multiplayer game has at least one of those things.