You're going to have these kinds of issues with any new or relatively new communications technology. Usually it will be much more localized than the Skype incident, but it happens all the time.

The terrible monolith that was AT&T, which just happened to deliver the best, cheapest, most reliable phone service in the world, spoiled every American born before The Breakup. The vertical integration they had allowed them to invest in levels of redundancy that ensured their services were almost never unavailable, and most of our telecom industry still runs on that infrastructure. Now, after the government has done us the "favor" of opening the industry up to competition - with the resulting increases in rates and reductions in quality - telecoms are faced with razor thin margins and huge marketing expenses which have made investment in quality and redundancy next to impossible.

Cell phone service is pretty much treated as a luxury. I live in an area where the backup batteries for the cell towers can keep service going for 4 - 8 hours but the typical power outage is measured in days or even weeks. The money for backup generators just isn't there, and never will be.

As for Skype, one of 3 things probably happened. Either they made an upgrade to all their servers which had consequences they didn't or couldn't test for, their servers got hacked, or the clients themselves were hacked over time and the time bomb went off. It's not a problem with internet phone service per se, but with any architecture where there is no localization of service, and that's going to become more and more prevalent across all communications technologies as time goes on.