You know what I love? Dan ("Delta") Collins's Original Edition Delta rules. You know why? Because he provides a massive number of design notes explaining exactly why he has decided on these particular rulings for his personal D&D game. Sometimes he references later D&D texts (his foundational system is OD&D); sometimes he references his own blog; sometimes he references specific historical treatise or reenactments.
This is awesome. This is what I want to do. I want to "footnote the hell out of" my rulebooks so that every time I get some random idea or notion I can check my notes and see EXACTLY WHY I made a decision to go the way I already did...and put the matter to rest.
It doesn't mean you can't change your rules later on! Listening to Dan's and Paul's webcasts, Dan is often heard taking to heart tweaks and modifications Paul has found useful/helpful in actual play, and added or updated his rules because of it (Paul is also using OED for some of his games, but with personal modifications). To me this is perfectly acceptable; even when a new rule or system appears to work well in play, over time it may shape your campaign in ways you don't necessarily want.
[a quick example...and one NOT incorporated by Dan...comes from this recent podcast: Paul's critical hit table, based in part on WHFRP's system, resulted in every PC in his campaign having some number of amputated limbs by 5th level. Amusing though that might be, not every DM wants a motley group of peg-legs and hook-hands populating their game (I did that back when I used to run ElfQuest...gets old after a while). It actually shaped the tone of Paul's campaign, and he has since reduced the chance of maiming]
Just having a "bible" of sorts that explains your rules is an idea I find incredibly useful. Yes, it can be time consuming (check out Tao's Wiki if you want to look at a more massive example)...but just having the reference available must be invaluable in the amount of time you save: seeing that note by the text means you have examined the rule, tested the rule, reasoned why you want the rule the way it is (either to model something specific or to better facilitate play)...and then you can just leave it alone. And if questioned by your table you have the explanation right there to point to...though I'd suggest holding all questions for after the session concludes.
I really need to take the time to do this. I balk at making the effort because I realize it will be time consuming. But it will save me so much time later...once I get back to running a regular game. Best to get as much ruling out of the way now, so that I can focus on playing when the time comes.