Since all the 3gs had sold out at the Apple store I went to (Pentagon City) within a couple of hours, I cannot see any conspiracy just because the 16s sold out first.
They could have had fewer 16s on the first day as a business decision because of market research or assessing the mail order patterns. Also they may have thought that someone going for the lower price point would go for the cheapest 16 wifi and would not spend another $130 for the 3g. Maybe they thought the 3g buyers were more likely to want the 64 or 32s. When someone is already paying $700 for an iPad, it's a big purchase, and paying another $100 for the 64 is not a big disincentive to get an iPad with more storage on the first day. Finally, as several people have mentioned, a person can still get the 16 3g by ordering or waiting for restocking.