I could modify the rules to reflect what I want. It wouldn't even be a big change, just a tweak to a mastery ability that none of my PCs currently even use. However, in doing so I add complexity to my game. I take it a step further from the base game, and in doing so I make my game less accessible.
Some of you are likely scratching your head and wondering why I care about the accessibility of my game. The problem is this: when you agree to run a game with people the only common thing everyone has is the rule book. Every step you take away from that rule book is a step you take away from that common ground. It is one more thing that someone new to the game has to pick up and learn. Quite literally, it is another barrier to entry to the game.
But A Table Top Game Is Pretty Small
This is a good point, and is ultimately the reason why I will likely go through with it. It is also why I've gone through with other rule changes I've made in this game. I have six players, I speak to them all personally on a regular basis, and I can explain to them any changes I've made to the rules and/or remind them of them in play. However, I've also spent a good amount of my time GMing running much larger games, and so I always consider that as well. Simply put: the larger your game, the less house ruling you can get away with without running into problems.
Store Games and New Players
Something else to consider is for anyone who runs their table top games in a gaming store. Odds are you'll have players drop out. Odds are that you'll also have people ask if they can sit in and join. One of the awesome things about store games is getting to meet new people, but that is also one of the most dangerous parts about store games too.
This is where house ruling can quickly become excessive. It's not just because the person has more to learn either, but that you have to explain it and what it all means for characters they want to play.
"Keep It Simple, Stupid" is a good maxim to always keep in mind for these kinds of things, and it goes both ways. On the one hand there is no need to over-complicate a game that is being run and going along just fine. On the other, there is no need to look for reasons to not do something if you think it will be for the better of the game.
Just remember: the more you change, the harder it is for people to just jump into the game and play.