This first wave was to gauge interest and build hype. It came out early November and made people want them in the lead-up to xmas. If Nintendo weren't still living in the 80s they would have a very large burst of stock this week, but so be it.
The next big wave is going to be mid-December when parents (and loved ones) are buying gifts and want "the big thing".
Then we'll get a large wave in early January for all the people who get cash for xmas.
And then we'll just get a continuous stream so that every sane person can buy one in February or march
As for why Nintendo does it this way: it lets them tell their board that they "won the holidays" because they had the must-have product. And next year they'll have the snes classic (or nes classic 2 if they can find more games). They make less this way, but they can pretty much guarantee they turn a profit and have good stories for shareholders.
As for direct shipping: Part of that is Nintendo not really having invested in the infrastructure for that scale of direct orders. But I suspect a big chunk of this is Nintendo trying to earn some good will with retailers who have dismissed them due to bloated stocks of wii Us, 3dses, and amiibos. Because Nintendo need to push the shyft and while they may think they can win with a Vita they aren't dumb enough to forget that retailers killed the psp go.
The target demographic with money today matches exactly with people that played those games as a kid. A lot of people would "pass" on the legacy looking console at a store but would tap away $5-10 on a phone without thinking about it.
I really hope they step out of their closed garden and port more games to iOS/Android. Mobile games can be the gateway to more people buying their systems, old or new.
As for why they don't raise the price and sell directly, you can ask this about every company that doesn't sell their products directly. Why don't they do it?
I would guess with this particular product for Nintendo is not really about the money. A company never wants to depend on profits from selling nostalgia alone, they want to look forward and grow and make new things for excited, engaged customers.
As for selling directly, they don't won't to burn bridges with retailers that still have a large role in pushing their products.