For many people, it's an issue of price and accessibility. The Virtual Console is available, but software titles are limited to a specific system (Wii, Wii U, 3DS), and many titles that are available at one location are unavailable at another. Secondly, the price to download a single game is rather expensive, at $5 per NES title. Third, Virtual Console suffered from a lack of exposure. Nintendo and other software developers never offered any promotion beyond the occasional press release. Finally, I don't know what the online shop on Wii U and 3DS was like, but the Wii shop channel was poorly designed and not very user-friendly.
For the average consumer, the NES Classic is an easy way to play classic videogames at a reasonable price. And you get a pair of oldskool controllers as well, which is very nice (I especially enjoy that the NES/SNES controllers can plug into your Wiimote).