I'm gonna poke my head in here, I was a major part of the rule making process, I myself, had to climb the tallest mountain in South America. I had a homeless man from scandinavia drink the milk of a coconut that originated from the oldest palm tree in Florida. (Shrain pulled the short straw on that getting that coconut, have him tell you about sometime) and after that, I was visited by Arceus' spirit messenger, George. Nice guy.
After these quests, we sat down, and brainstormed ideas that we thought should or should not be allowed, in fair interest to all. We decided that certain combos, such as drizzle+swift swim and Sand rush+sand stream should be banned, while their alternate type counterparts (chlorophyll, for example) were fine based on ease of use. There are a lot more possibilities to "abuse" those two than to abuse chlorophyll. Even smogon has drizzle/swim banned. We chose to just ban the combo instead of individual pokemon though, because we want to keep rules simpler than "these seemingly arbitrary (for someone not in the metagame) pokemon are banned!"
The limited and restricted list we tried to keep simple to explain as well, for similar reasons. We picked pokemon commonly banned, and then based on their "potential", narrowed it down to what we decided was easy to remember (you will notice that these lists are almost entirely "legendary" pokemon) While we do have a lot of pokemon not shared by the Official Pokemon rules, or Smogon, that's because through our playtesting we determined it wouldn't be...sporting, for lack of a better word.
There are some rules that not everyone agreed with, and some feelings were hurt, but this is what we decided after WAY too long. We may take into considerations for revision that anyone has, depending on how things go and if people REALLY don't like any of the current rules.
I hope this wall of text helped, please feel free to PM or just post somewhere if you have anymore questions.