These stats seem to cause more problems than any others, or is that just me? Presence if low is often interpreted by players as being ugly or intimidating, but actually it seems to be making no impact - more like Halo Jones from 2000AD?
Also there seems some confusion about when Presence and when Communication applies to an action. Do other people find this or is it just me?
low stats are, by definition unimpressive. A person with low presence isn't epically ugly and intimidating- they may be ugly but it is more the leper that everyone avoids rather than the scarred up warrior who is scary and repulsive. The warrior actually has a high presence.
IMHO low Presence isn't intimidating - at least not when you want to be - because it's the stat I'd use in a Leadership roll to be forceful. Instead low presence is boring, unimpressive, uninspirational and with a tendency to convey the wrong message at times.
For my group I think we tend to use Presemce for here-and-now social rolls, while Cmmunication if for when you have a longer time to work your social engineering. When you have time to use clever words and phrases rather than relying solely on charisma
I admit, I have had some fun sidestepping this issue with generous applications of classist physics. I don't do this in most games, but sometimes I decide to accept shame for the sake of trying interesting things. For example, a favorite houserule of the other troupe members is "inner beauty matches outer beauty," so all physically attractive characters are charismatic and of high mental caliber and all charismatic or mentally capable people are also attractive. They like it even more when that's combined with a houserule that gives peasants "free" Weak Characteristics, with those of higher class standing (nobility, clergy, and magi, mainly) get free Improved Characteristics to reflect their native superiority.
But that's just because my troupe likes to be cruel sometimes...
Somewhere along the line, I picked up the heuristic that Presence covers in-person interactions, while Communication is used for written communications. I don't follow it strictly, but it seems like a reasonable guideline for most cases.
I hadn't thought about a specific way to rule, but doing so now I would tend to go with the response you're after. If you want something more emotional, Presence. If you want something more intellectual, Communication. So intimidation, being a response of fear, would use Presence. Meanwhile teaching, being about understanding, would use Communication.
If it's written, it's Communication. End of story.
In person, it's a lot fuzzier. In general, emotional responses are Presence, intellectual are Communication, but there's so much overlap that in most cases I'd let a player use either unless the situation clearly called for one or the other. For example, if using Charm to seduce someone into bed for a night, Communication would rely on witty conversation, while Presence would rely on physical attractiveness or earnestness (courtly fine amor should be primarily Presence).