For me, shinies are way easier. Across my playthroughs, I've encountered wild Shiny Golbat, Surskit, Fearow, Luvdisc, and most recently a Whismur. I encountered a Shiny Charmeleon from the Battle Factory Pokemon selections, and I encountered an opposing Shiny Kingdra in a Battle Tower challenge.
I had to trade a Pokerus-infected Pokemon from someone else's copy of Ruby Version to obtain the Pokerus status. I've never come across the Pokerus in my own personal playthrough of Pokemon games... A bit annoying, and I have to check whether I still have a boxed Pokemon with Pokerus somewhere...
Mirage Island is a whole 'nother story. -.-