Basically, I mean pokemon shouldn't be quite as clear cut as to where they appear Something like: 1% chance to run into a pokemon that's supposed to appear 1 route away .1% chance to run into a pokemon that's 2 routes away .01% chance to run into any other pokemon (That's available in the wild)
It wouldn't be a big difference, but it would be kind of cool to have slight blurring between the routes/caves (And the probability of finding one from >2 routes away would less than the chance of finding a shiny, it wouldn't mess with much)
Currently awaiting: Pikmin 3, Lunar Knights 2, LM:DM, AC:NL, XY, X, WW HD, LoZ U, LR:FFXIII, FFVXIII Skarmory would slap the hell outta you
Considering that finding shiny Pokemon is so rare anyway, there is no need to change the rate at which they appear. Also, your percentages for encountering this Pokemon are uselessly low. Why not just not post your idea if you want the chances to be that low?
No, I think it's a really good idea to have Pokemon spread out among the routes more. There is done of that, but they should do more. Just no Pokemon that would never leave their habitat, like cave Pokemon.