The problem is that, as your game goes on and comes into development, you find all of these little snags and loop holes you want to include. Narrative structures that you want to have the game able to support, or just little nuance details that you feel need to be handled. As you try to address them, even with larger things you do need to have, you are constantly adding more and more rules into the system. With each rule, things get more complex, there is the possibility of another loop hole, another possibility of two rules contradicting each other, another chance of confusing anyone who is trying to simply follow along.
Essentially, every rule you add, adds complexity to the game. Make a rule for reloading faster than normal, you have just added another complexity to the game. Make a rule for how bleeding works, the game has just become more complex. This is one of the key problems with a lot of RPGs that were made in the 80s and early 90s, in their attempt to simulate life, and give rules so it was clear just how things interacted the systems became very complex, bogged down with the rules that were made to help things go smoothly. It has been subverted in a lot of more recent games, though sometimes at the cost of over-simplification of things (I'm looking at you Crafts skill from nWoD).
The worst part about this is that you, as the maker, will probably not see the confusion this maze of rules can cause. You know how it all works, how it interacts. You know the reasons why each piece was put in where and how it was put in. To you it all makes sense, because you made it, and it is clear cut where the rules (in a by the book reading) give power to the GM, and where things are more specified. This is why sometimes video games come out with non-intuitive control schemes, after working with it for 2 years the Dev team and QA team find it perfectly intuitive because they know exactly how it works. The new gamer though may not.
All this is why, as you go through revising and adding things to the game you should remind yourself at times to just Keep It Simple, Stupid. Go back through sections you've finished, and try to read them as a fresh person to the system. Better yet, try to explain how things work to yourself as if you knew nothing about it. If it gets confusing, or hung up on things, maybe you should look at it, see if it can't just be removed and left up to the GM, or put in some other way.
Refer back regularly to your core wants for the game and the system, if you can strip it down to that core. Everything else is essentially just add on, so go back to the core and see what needs to be added on to the game for it to work, and what doesn't need to be there. If you can, unless building the game for a much larger crowd, maybe give the GM the say over how things work so it can be tailored to their game.
Those other rules and ruling you are ripping out? Don't throw them away, especially if they work. Use them as a basis, you might find you do need them later. If you don't, you can always use them as optional rules that can be thrown into the game for those looking for a more complex and detailed rule set. Throw the rulings in on side bars, and let people decide if they will use them or not.
Happy Gaming, and remember. Keep It Simple, Stupid!