I started running D&D 3.5 in a custom setting based on Garth Nix's Old Kingdom trilogy. It was really fun, but I needed to do a lot of creative work to make the rules of 3.5 fit the setting - change how races work, brand-new classes and skills, etc. When I moved to more traditional fantasy settings, I still saw a lot of bugs in the rules, things that didn't make sense or were just inconsistently designed (The Alexandrian's 'Calibrating Your Expectations' post really opened my eyes there). My houserules got pretty extensive, and when my group switched to Pathfinder and then Numenera, I kept finding things to improve or tweak. I ran LotFP for a year and really enjoyed it, but I also kept adding and expanding stuff as appropriate for my setting and the tone of my games. I did a lot of research and read very extensively in the RPG blogosphere to see what other people had done and why. Eventually, I decided to stop trying to substantially hack these rulesets and write my own; after 5ish years playing and running, I had run and played in a fair number of different systems and knew what types of resolution mechanics I liked and also had a pretty good idea as to some elements I wanted to explicitly incorporate in my game that I didn't see a lot of other systems offer in a meaningful way. I've been running my own system at my table for over a year now, and the rules are very different in a lot of ways than where I started. Some stuff has really worked, some stuff really hasn't. I'm blessed with several very ttrpg-knowledgeable players and some who were brand-new, so I get a nice mix of opinions that have been incredibly helpful to the design process.