I tried the bonus advantage thing for Presence once, didn't really like how it worked out in practice. The one I had settled on when I was still using Abilities was for each rank of Presence to give a bonus skill point that could only be spent on Deception, Intimidation, or Persuasion (or maybe add Expertise and Insight to the list). It's still a little paradigm-breaking, but it does okay.

You could simplify it by just saying the Presence bonus is doubled for whichever social skill you have the most ranks in (choose one if tied).

I had also come up with a custom Benefit that eased the issue with multiple lower social skills usually being worse than a single high one:

Benefit (Social Butterfly): When interacting with others in a manner where multiple interaction skills can apply, you may roll multiple ones, and the subject's reaction is whatever would be most positive for you. Usually, that means based on whichever roll was highest, but not always (if the higher roll faced a higher DC, for example, or that skill would lead to a less favorable result such as Intimidation only making the subject angry, a lower roll might be used). You may roll up to two qualifying skills as long as both of them are at least rank 5, or up to three if all of them are at least rank 10. The skills must all be valid based on your interaction; you could use both Persuasion and Intimidation if you are making a "carrot and stick" offer, for example, or informing them of something bad but also offering to help them avoid it, but you couldn't just make a straight threat and then roll both.