First, the familiar cards concept, while an interesting idea, needs to be brought to the attention of people. I am getting absolutely sick of playing every game with the same base cards, especially Chapel. Chapel just stops being interesting when your last 6 games have also had it. I personally marked everything as familiar because I don't want to be gently led into all the cards that have been released since Hinterlands (the last set on Isotropic). If people aren't actively marking cards as familiar, the feature is very very annoying to people like me. I think maybe it's better on Good Match than Quick Match, but if that's the case it's not very clear, and I'm worried since I didn't play on Goko/MF that Good Match will be matching me with mainly newbs and I won't get to see decent players actually using all the new cards.
We're trying to improve here. Up until the last release (~20 hours ago) the matcher ignored familiar sets (even on good match), but now it is:
The matcher counts the number of cards you have both subscribed to and marked as familiar. This set is called your "expected" set.
For a possible candidate, it counts what percentage of your expected sets are marked as familiar by them. A bonus is added to this of 10% times their setting of "max unfamiliar cards".
If the resulting percentage is less then 80%, you will not consider them a good match.
I haven't really documented this yet because it's very likely to change again in the near future, and to become user-configurable later on.