Skype has been in the news recently with allegations of ties to the FBI and NSA. And a list of other security concerns listed here:
http://en.wikipedia.org/wiki/Skype#Security_and_privacy
I know that if I had no other influences, but needed a product like Skype, that alone would be enough to consider other possible options.
The wikipedia document also comments that Skype utilizes RSA key negotiation and encryption technology. RSA is also getting bad press currently.
I, personally, have never used Skype, and as such have no opinion as to the quality of their service, be it good or bad. You have stated it to be good and I have no reason to doubt your comments.
Unless either forced, or under duress due to unforeseen circumstances, I would never use Skype due to their ownership by the evil empire.