Hey op I feel your pain!!! Ive come to commiserate and join in your rant! Reading your post was like reading a list of my own experiences.
I had a perfect workflow with XDK, then had to migrate to Cocoon same as you. Discovered there was some bug preventing data being written to localStorage on iOS, so was just unable to update my game for iOS... Apparently that issue *may* have been resolved (I just checked on the cocoon forum and some new info has been posted since I last checked) so I guess Ill go try again when I have time.
I'm not a huge fan of Cocoon tbh (I preferred XDK). I am considering whether to move over to either C3 build service or maybe Cordova CLI, and compile on my own PC? That might be a good option.
One thing Ive learned is you have to be meticulous with note-taking. Exactly for that situation you described where you manage to export a working apk / ipa. Then next time round you get a failure of some kind and you can't remember how you succeeded previously because there are so many bloody variables involved that its impossible to remember everything.
Now I make certain to write down my work flow... step by step, so I can always come back to it weeks / months later and achieve the same result. Its imperative. I have a crappy memory at the best of times, so if I don't write it all down Im bound to forget. I use OneNote for recording all my game dev notes.
Oh and I tried that Appodeal ad plugin too. I was unable to get it working how I wanted so I ditched it. The two plugins Ive had success with are the Cranberry Chartboost plugin and Verstala's adnetwork mediation plugin. But of course both took hours of fiddling and troubleshooting to make em work.
Id say don't give up your game dev. You have to keep at it. You just gotta get a good work flow in place. Like you mentioned, once youve got a good work flow sorted out it can be reasonably straight forward to get your game built (although I agree there are waaaaay too many steps involved... its even worse for iOS!).
I think charging a flat fee for your app is a reasonable idea, and easier obviously because u dont have to stuff around with ads and iAPs, but I think it can only work if you can figure out how to direct traffic to it. If you can generate a user base on your free games first, you may be able to persuade them to buy your paid games too. Otherwise you are relying on people finding it organically or being featured or something. Id say you have the right idea about trying to get a few f2p games with ads published first.