Primarily the single vendor lock-in.
You can achieve exactly the same with SIP - however since SIP by nature is more centralized the latency issue Timmmm (636430) mentions can be a problem.
With that said I don't have anything specific against Skype - it works, and people are happy so hurray!
However I disagree with the quote - carriers should be providers of dumb tubes for the customer to transfer bits, however they have used an excessive amount of money on "smart pipes", which main purpose is to help the carrier overcharge for certain kinds of bits.
This of course is stupid, and a prevailing open standard which helps relegate carriers to be only that is helpful here, and Skype does not do that, on the contrary it works against this.