My biggest problem with Parelli is that they are no longer concerned about the horse, but about making money. It turned from a fairly decent training regimen into a money machine. My next biggest problem is the idea of your horse being your "friend." This in and of itself is dangerous. Your horse doesn't want to be your equal - that's not the way it works in nature; horses use a hierarchy and live by it. They need a consistent leader (you). Being your horse's "friend" puts you in a dangerous position, because if you don't establish yourself as the top dog, your horse will, and that's a situation you don't want to be in.
Another thing is, Parelli does not advocate helmets because (and I don't remember a direct quote, but it was something along the lines of...) "by the time our trainers are ready to get in the saddle (which is three years, by the way), the horse is so well trained, the rider doesn't NEED a helmet," which is wrong, wrong, wrong! I'll admit, I don't wear a helmet every time I ride, but to flat out say, "nah, you don't need one" is just messed up.
I've worked with three horses trained by "Parelli Instructors", and every single one of them has been ruined. Case No. 1: Diamond. My instructor's mare was sent of to a 4 star certified Parelli instructor, because my trainer was pregnant with her first child and was too far along to start the mare. When Diamond came back, she was spooky, would not let anyone near her in the field, attempted to climb out of the round pen, and only feels comfortable around people when they're on the other side of her stall. Case No. 2: Friday - MY horse. He was trained by a local woman who is NOT certified Parelli before I bought him. He seemed okay, but he's extremely hard to train, always looks around under saddle, ignores you, get frightened immensley by whips and crops, will not lounge at all without throwing a fit. Case No. 3: Spiderman - a walking horse trained by a Parelli follower (I'm not sure if they were certified or not). Spiderman was afraid of you if you waved your arm. Would not be caught in the field, and bolted at the slightest movement of your body (but was okay with tarps and hula hoops, at least!). I had to retrain him for a university class, and it was a nightmare. By the end, we found trust in eachother, unfortunately the person who bought him suffered from a broken leg caused by Spidy, and I think, but don't know, that he was sent to slaughter.
On the flip side, I saw a young Parelli enthousiast train a horse at the same university with a mixture of Parelli and cowboy techniques, and he turned out beautifully. Just, I've not had good experiences with Parelli. Maybe I just got to know the three worst Parelli-trained horses ever, but it seems like an odd chance that the only three I know are basically crazy.
EDIT: Also, I know for a FACT that Parelli doesn't always abide by his own techniques. He came here for a clinic and I saw him behind the arena working with his stallion. Instead of being passive when he misbehaved (which is what he preaches), he got onto the stallion and shanked him and gave him proper discipline. That, to me, justifies the fact that he doesn't care about what he tells people as long as he gets paid.