The Wii Shop Channel has the most virtual console games at the moment, spanning the NES, SNES, N64, Genesis, and more. You can't buy full retail Wii games from the Shop Channel and your games are restricted to 480p. The Wii U eShop allows you to buy and download retail games to your system. The virtual console is far less diverse, but there are some differences, such as GBA and DS games. A handful of Wii retail games are available, too. Virtual console games you get from the Wii U eShop are displayed in 1080p with the exception of Wii games(upscaled 480p).
With the Wii U, fortunately, you can access both. You can upgrade a purchase you made in the Wii Shop Channel, should the game ever come to the Wii U eShop. For example, I had purchased Super Mario World in the Wii Shop Channel years ago. When it became available in the Wii U eShop, I was able to buy that at a discount.
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