Hmmm, that's an interesting question, but here's my take on it, since the champion is never officially an elite 4 member, not to mention in the first Pokemon games, red and green, when you beat the last elite 4 member, lance, he states that after blue, or Gary, or whatever beat him, he officially became champion, no mention of a previous champion, meaning that the elite 4 originally didn't have a champion, otherwise there would have to have been someone after lance for Gary to fight, but since there wasn't, that means there was only 4 members originally, hence the name, elite 4. One more example, this time as to why the don't replace one of the elite 4 members with the champion to get keep the number to 4, well, inevitably, the elite 4 would be made out of 4 Pokemon champions which would be, let's face it, a bunch of 10 year olds, and while they would have enough skill as a Pokemon trainer, they simply wouldn't be mature enough, or old enough to run the elite 4, which is why they use 4 highly capable adults instead.
