It looks like the favorite sites are sorted by reputation and the feed picks up on this as well. Fair enough in general, but for me, it's definitely wrong. I used to be reasonably active on SO and am still accumulating plenty of reputation from old posts there, but now I'm primarily active on cooking. I can't actually tell whether it's using total reputation or recent gain; I still gain plenty from old posts on SO.
The favorite sites and feed should use recent activity for ranking, not just reputation.
(I found this question, but I'm definitely suggesting automated selection here, not manually curated tag sets.)