The "rarity" argument doesn't quite hold up for me, because there are metavariants that should be equally rare that are bargains compared to the baseline metatype. Wakyambi and satyrs are both bargains, getting 10 points' worth of positive qualities for a 5 point increase in metatype cost. Oni cost 25 points more when the only difference between them and standard orks is a disadvantage. Ogres cost the same as standard orks and get an extra advantage. You can't even factor in "they stand out in a crowd" for all of the metavariants, since ogres and fomori are actually less brutish in appearance than standard orks and trolls.
In short, if you look through the metavariants, some of them are very cost-effective to play, some come out about even, and others are overpriced for what you get.
I guess it doesn't bother me as much because I am not really that interested in the ones which happen to be gimped. If I were GMing and a player complained, though, I would probably drop the costs for some of the worst cases, such as oni or xapiri thepe.