@slayemin, Firstly, thanks for your input and feedback. My argument wasn't against prototypes per se - it's more against the ideals passed on in guides. Reading 'getting started' guides, I was left with the impression that game development was a process, bombarded from all sides that linearity was key.
In my case (Winter's Coming), prototyping involves me finishing the physics engine first. While there will be prototyping, I'm holding it off until the engine is polished - I believe my game's mechanics will be interesting, so only some tweaking will be necessary. I'm mostly interested in physics games right now, so the physics engine will still be a must.
Regarding the 'zero days' - I agree with you completely. An addendum to what you said is that before going on your computer or laptop, before booting the engine, set clear goals. Ask yourself what you want to work on, before the internet get its grips on you and you end up procrastinating.
Maybe you find this helpful/related:
http://www.gamasutra.com/blogs/EthanLevy/20140320/213611/Escaping_the_Indie_Shame_Spiral.php
The general idea behind prototyping is that you never know whats going to work and not work right when you enter into a new game project. Rather than expending enormous amounts of effort building something which turns out to not work, you can throw something together as fast as possible and see if it all works together (ie, game mechanics). If it works, then you can either throw away the prototype and build the real thing, or use it as scaffolding which you fill out and polish. Prototyping saves you time by helping you avoid traps early.
Sure, you can rationalize this away as "just another voice to ignore", but some of these voices are borne out of hard experience and are trying to help you avoid repeating our previous mistakes.
My best bit of advice... Don't have zero days. A zero day is a day in which you accomplished absolutely nothing. Zero progress made. Even one line of code is better than none. Make a little bit of progress every day, and given enough days, you'll get there.