Ok, so this is my full report from San Ysidro, California:
-Toys R Us: No Math, Villager or WFT, Samus and Fox where down to about 4 or 5, everything else had decent numbers.
-Target. Had everything at least 2 of everything, including Marth, Villager and WFT (2 each) but they only had a few and they are also the most expensive place to find amiibos. They told me that those in the aisle where all they had when I asked for other since I wanted to find a nicer looking figure for a friend.
-Wal-Mart. Absolutely destroyed. Only Mario, Pikachu and weird enough, one Samus and 3 WFT, apparently only collector are interested in WFT. I catched the guy just bringing in the last they had, namely MORE mario's and pikachu, a peach and a villager. Took the last two.
-Best Buy. They had nothing at all. They hide what was left on the counter and you had to actively ask for them, I took another villager (the only one they had) and saw only one fox and one link left there. They may restock later.
-Gamestop. Went to 3 different ones and they only had for preorders, or at least they told me that, asked me to come back next week but refused to tell me if the rare ones where going to be available. Preo-ordered Shulk while I was there.
So all in all, I think the worst selling one is going to be WFT, it is not stocked plentifully, but when it is, they seem to not be sold as fast as the other one. Getting a Marth or Villager is going to be the hardest since they do have demand from people who are not collectors (At least two people asked for them while they where buying just one or two amiibos, not all of them), and Nintendo may not produce more. Hopefully they do.