I prefer 1) Group Points then 2) Points Difference. Because it's simple. I like Group Points because that emphasises winning. I don't like Direct Encounter because it only works for 2 people in a simple way.
But, some games or pairings of player give rise to small scores when the game is played conservatively or defensively and others lead to high scores when play aggressively. When everything else has failed and I am clearly behind, I'd be happy to take a huge risk to try to win a game. Most likely I fail then my opponent might go from a small but definite points difference to a huge one through no skill on their part. Just saying.