I wouldn't really want my Pokémon in X and Y to get non-beneficial viruses, especially if one of them gets one somewhere unexpectedly at the starting points of the game; that would be really unfortunate. But if there are more beneficial viruses other than Pokérus, which enhances your stats by multiplying the EVs by two, then that will be a good idea.
Let us say, other than Pokérus, there are other viruses that'll enhance or boost one stat only; that's good enough for starting trainers. And also, the beneficial viruses would be a bit more common, while Pokérus will be the rarest of all viruses. More than that, I think there should be different viruses in different areas of the region, just like how there are different Pokémon in different patches of grass of the region. Just to make thing fair.
But anyway, if you've read my first sentence, it doesn't mean it's a bad idea to have non-beneficial viruses in the game; I just don't want to have my Pokémon have one at the beginning. So, if you've read my fourth sentence in my second paragraph, I stated that it'll be good if there are different viruses in different areas of the region. If that's the case, the beneficial viruses will be the first ones to cling on our Pokémon while the non-beneficial viruses will be introduced later in the game, post-story perhaps? They would be a bit less common than the beneficial ones though. The introduction of the SecretPotion again and other possible medicines and herbs to heal those negative viruses would be introduced too sooner in the story of the two games.
Anyways, that's just my thoughts and ideas. X and Y is more speculated to the XYZ axis though, but the idea of chromosomes are also quite fascinating, and would make the games more interesting.