Richard,
As far as what I would get to start is a bit of personal preference. I have flown most of the major flight controllers except DJI stuff. Because MK has served me the best and has ALL the features I want and need that is what I have stuck with. Yes it has a steep learning curve, is very complex, and reports of some hardware quality control issues. I have had a few issues with MK BL hardware BUT I have never had one fall out of the sky or fly away like other FC's I have flown. I also really like all the telemetry available for MK beyond their ground control station. I am most impressed with the Graupner MX-20 telemetry system with the smart box add-on.
Some questions you should ask yourself before taking the plunge:
1. Are you mechanically, technically, and electrically inclined? You or someone you know is going to have to be able to work on the thing at some point.
2. Do you have a good bit of time to invest in learning to fly?
3. Will you have the $$$ to invest in the future for doing what you want to do?
If it were me I would start with the Aero-SIM RC program, an inexpensive transmitter that will work with Aero-SIM and most MR FC's you want to get. And then you have to decide whether you go with something like a blade mqx, MK basic quad, or one of the DJI Naza based quad kits to learn to really fly on. If it were me I would do the MK because it is easily upgraded to a full navigation capable copter with the addition of the navi board and gps. If you get the MK kit the build is well documented and there is a lot of help available on this forum. Others may recommend the DJI system and can provide you with better details about it. If you are serious about doing this then you should plan on spending more like $2k unless you just get something like the blade mqx, although this won't allow you to start learning an FC system that can grow with you.
My 2¢!
Shawn