There are good ways to create house rules and bad ways to create house rules. That's why some people love house rules and some hate them. Generally it depends on which end of the house rules you're on as to whether you like them or not. I'll start with the bad way first, because that's how everyone actually does house rules:
A GM, after having read a game and before playing it (or after playing it but before a current group plays it), thinks something systemic is messed up and "fixes it". I used to be this guy. Pretty much everyone is this guy. All newbs are this guy. This guy is an idiot who doesn't know one fundamental truth.
The rules aren't for the GM. They are for the Players. The GM lives and plays outside the rules. The rules themselves effect the GM in no way at all. Don't focus on them, it's a waste of effort.
If you find yourself designing house rules before playing a game that's fine. It can be fun. Don't use them on the first session or any random session you have with a group. If you like a game you'll play it without your house rules. If you find you can't, that's a hint that you don't actually like that game, just elements of it.
So, play that game Rules As Written (RAW) and wait. I'm serious, wait. Don't discuss house rules, don't worry, be happy. Wait. If there's a real problem with the system, your players will tell you. They'll bring it up when it becomes an issue, or after it becomes an issue during session wrap-up. If it's not bothering they who have to play by the rules, it shouldn't be bothering you, who doesn't.
This finally brings us to the good way to design houserules - do it for system issues that the players arise that you agree with. Present your solution, which may indeed be one of the rules you built and had in a 60 page binder of houserules for the game you're running. If you don't agree with them, explain why. Have a reason, because they will have reasons to change it. If you don't have a reason to keep it as-is, then change it regardless of your feelings about it. Because the rules don't affect GMs.
