Why is it? Technology has progressed enough to the point where "owning" something is basically a right to use anymore. Paying $50 or whatever back in the day, for about $70 inflation nowadays to play SMB 3 and paying another $30, $35 on GBA sounds like a right to use to me. The Virtual Console version is EXACTLY THE SAME as the NES version, so they're essentially charging for something you already have a right to use.
How would you like it if you had to buy a different DVD for every brand DVD player? Pretty ridiculous sounding, but this is the same exact shit. Just because the Wii is a different system than NES doesn't mean you don't own the same exact right to use. Not to mention all the people who worked on the game back in the day, who aren't with the company, likely aren't being paid a damn thing for their work based on the digital downloads.
Typical consumer exploitation, and I don't feel a damn bit sorry for their so called "piracy" problem.
Don't buy it then, I own plenty of NES/SNES/Genesis/etc games and I don't buy the ones I own, or the ones I know I can get cheaper off ebay... but sometimes, it's worth buying on VC because the game is much cheaper (11 bucks for Sin and Punishment, 9 for Alien Soldier) or because the games run better (N64 games in 480p with ironed out framerates). I don't see any problem with the core concept of the VC, there are a lot of side elements I'm not too happy about tho, namely the 1-2 game a week we've been getting lately, and storage space.
Region-locking games is bullshit, though.