I'm pretty sure I remember reading that (in Japan at least) Nintendo is pricing the eShop versions below the MSRP -- in fact, I think they were pricing them at ¥4580. That means retailers are pricing their products lower to compete with Nintendo's price. Nintendo isn't "sucking at online services," they're competing with retailers, resulting in lower prices. Which sounds like a pretty good thing to me.
Not completely sure, but I read that on e-shop is the exact same price, full price.
Don't get me wrong, I don't think that Nintendo has a crappy online service, just expecting some people which would take advantage of anything to hit Nintendo.