There can be no doubt that Nintendo completely dropped the ball with the Virtual Console. Infrastructural issues such as a lack of unified accounts leading to repeated purchases of the same software for each new hardware aside, Nintendo handled the release schedule very poorly- they have the richest back catalog in all of gaming, but they staggered releases until the service lost all steam and interest, and no one cared.
On the Wii, it was still handled somewhat decently (although the N64 selection was shockingly lacking); on the 3DS and Wii U, it's an embarrassment. Add to this something as stupid as Nintendo's emulators lacking in basic functionality such as optional filters, and it seems like the ball was dropped completely.
Meanwhile, while Sony's handling of PS Classics is commendable by comparison, let's look at PlayStation Now instead- an on demand subscription based service that promises access to all PlayStation classics across all currently active PlayStation platforms, and even non PlayStation ones (which Nintendo should have done). Is PlayStation now, as currently pitched, what Nintendo should have been going for with Virtual Console all along?