Indeed, the only reason for them doing that is because most people these days would simply give up an hour into most NES games, and so this gives them a chance to beat them without actually having to put out much effort. And, by doing that, cheapens beating any game on the VC, and completely removes the possibility of any real score challenges between people.
Hm...I think Nintendo should try to address this because legitimate score challenges in basically every old game would be great, but I'm not sure of a good way.
Maybe choosing competitive or casual on some sort of pre-game menu, and having the version show up on Miiverse screenshots somehow? It would be bothersome to those who don't care though, so maybe only do that on first play and hide it in the home menu or something. I dunno.