I've been doing no planning at all. I've literally just took the one step at a time approach, set a short time goal, implement that feature, on to the next. Then when I'm done with something and I move on to the next, something just randomly clicks and goes, well if I'm doing this I should've just done (something I've already done) this way to make it better.

Well I've been programming games this way for over 15 years and it works fine for me. My prototype and plans are in my head, and I only resort to pen and paper to visualise particularly hard concepts, rarely. This works fine for me and I have no need to change my ways, but it might not work for you. Do what works for you and try some different approaches as people have suggested here.

Good luck!