Since dronekit is more directly involved with ardupilot project it is the one that I would trust more to spend time on developing on, particularly if you plan on running custom functions on your companion computer (raspberry pi).
However if building web apps is more your focus then I definitely say flytOS is the choice to go for as their webSDK makes for an easy starting point, also flytos supports a wider range of hardware. And the other key advantage of flytOS is that their API lets you run C++ or python, but dronekit only supports python for now. However that is not to say you cant run web apps using dronekit.
I will be curious to know anyone else's opinions, as I have not spent too much time with either, only played with both briefly to get them talking but have not tried to build any of my own apps yet.