Exactly. I used to houserule the hell out of 1e and 2e and it was easy to do without having to grasp the entire system.Each piece builds upon the other, so modifying one thing can have unintended consequences.
In 3e I only felt comfortable to slowly introduce houserules after I'd played the system for about two years. Only after that time I was confident I'd be able to properly gauge the effect of the changes I made.