So, here's a pair of hypothetical situations, let's look at one way of seeing the issue with characters with good ranks in intimidate. One will have high cha, another low cha.
1. An assassin has infeltrated a castle and is looking for Master Chen, lord of the mannor. He dispatches a guard, but is stumbled upon by a serving maid. The assassin pulls the sword from the guard, and gestures at the maid. "Take me to master Chen's quarters," he says, "or die."
The difference between the low cha and the high cha characters are fairly negligable (assuming decent ranks in intimidate). The circumstance modifiers and skill ranks will more than make up for a roll high enough to scare the poor girl. In the circumsatnce where someone failed their intimidate roll, the girl would probally scream, rather than being hypnotised by the assassin's actions. She'd be scared by anyone with a sword, but not necessarrally crushed.
2. An assassin has infeltrated a castle and is looking for Master Chen, lord of the mannor. He dispatches a guard, but is stumbled upon by the captian of the guards. The assassin pulls the sword from the guard, and gestures at the maid. "Take me to master Chen's quarters," he says, "or die."
The guard captian's obviously a hardened fellow, and isn't so easily scared. He might feel a little fear at the sight of a tough guy with a big weapon, but he's lived with that sort of thing, and trained to deal with it. The added cha might tip the balance here. Let's say it does. In this case, each person's threat rings true, but the guy with higher cha just has a little more poise, a little more confidence, and it might just be enough to push it over the edge.
Anyway, as far as the tough guy being more intimidating, I disagree. I also disagree that the guy with the higher charisma is more intimidating. It's the guy with the high intimidate skill who is more intimidating. Charisma can just help a little with that.