Got myself an used copy of Captain's Logs: The Complete Trek Voyages, because it was so cheap, but looks like I should have invested in more recent copy, this book is damn interesting. And even after being a trek fan for over 20 years, I had no idea of all the background stuff that happened in those early years. Based on this book Gene L. Coon had a huge role as showrunner during the later half of season 1 and the whole season 2, when most of the best episodes were made, and when the characters and the universe were defined better.
http://en.memory-alpha.org/wiki/Gene_L._Coon
Also the episode guide for the already written Star Trek Phase 2 episodes was excellent. Looks like they even used some of those episode ideas in Voyager...