I'm not sure why you're surprised.
CloudFlare is amateur at best, compared to existing DSA/CDN offerings from Akamai, Cotendo, EdgeCast etc.
But those cost a lot of money (at least 50-100x the cost of CloudFlare) if you're small/medium sized. You get what you pay for with $20/month.
The 3 second slow down looks like a standard TCP reset + retry. They're probably having issues with that particular POP. That it took several hours/days for the 'best engineering team in the world' to resolve tells you all you need to know about the service level you should expect from them.
But, once again, it's $20/month.
