I don't think Nintendo expected the Virtual Console to be as popular as it is. They were using it as a way to fill a digital release schedule that would go away once there was original software, but then everyone loved it and largely didn't give a **** about WiiWare and then Nintendo didn't know what to do.
Nintendo doesn't want VC sales to cut into eShop sales, which is smart for them because while VC is basically free money for them, third party eShop support will dry up if people are buying Virtual Console games instead of the new stuff. It's not a good idea on their end to release all of them at once, but they need to do better than the "one game a month" policy they currently seem to be implementing on the 3DS.