I do understand your reasoning and logic behind your belief. If you were to ask someone now: "What application do you use to video chat with?" the answer is most likely going to sway heavy to Skype. If you ask that question in 3 to 9 months time and that answer has not changed, then Skype will be just fine.

Personally, I don't like the idea of video chatting through Facebook. I use skype exclusively to video chat because its what I am accustomed too, it's the application I trust. Trust being the keyword there because I do not trust Facebook.