Secondary DNS functionality is usually implemented with AXFR which doesn't support advanced functionality like Geo DNS and also limits the providers you can choose as only a few offer it.

It also doesn't help with managing the records in the primary provider, requiring either working in a UI or writing using software like OctoDNS to manage it. It's definitely a good option for simpler and stable setups, neither of which is the case for us or many of the people I've talked to. If it fits a situation you have it's worth exploring.

There's an article on ZDnet, http://www.zdnet.com/article/github-open-sources-octodns-new... that does a good job of covering some of the reasons for it that is probably relivant to this.