I think the idea is that half-elves have to be a bridge between the species, or that to navigate the challenges of being a half-member of whatever culture they grew up in, they have to be extra charming. It's a little narrow, perhaps, but it always made sense to me.Diplomacy Mechanics were introduced in 3.5 to tart up the lacklustre half-elves a bit. I don't know where that idea specifically came from.
This seems to be something they're increasing in 4e, with mention of a half-elf's "inspiring presence" from one of the playtest reports. I think they'll have half-elves being natural leaders. Maybe they'll explain that as a positive trait that arises from the union of the two races. In the real world, I often hear comments that biracial people are particularly attractive or bright. (This is partially driven by the phenomenon of heterosis or "hybrid vigor.") Perhaps in the world of D&D, that notion is fact.
And half-elves are expected to be in the PHB, because they're shown in the mural in the inside cover of Races & Classes that has every other confirmed PHB race.