I found a great map that shows where to find all the pokemon in the game.. but how do I know which ones are the rarest? that way if i come across them i know to catch them

got a picture of it? I could go through the whole thing and tell you which ones.

if they are shiny or legendary they are the hardest to find

With GTS, Wonder Trade, and a slew of trainers breeding perfect IV's onto competitive Pokémon, just about every Pokémon on your map is common.
Not only are they common, they're weak and don't have the correct Nature.

Rare Pokémon: (A Breeding Guide)
Rush through the game to unlock Kiloude City. (There is a man in the town Pokémon Center who'll tell you the highest IV's on a selected Pokémon)
Attain a high IV Foreign Ditto, Destiny Knot, Everstone, and a top tier Pokémon (Charmander, Frokie, Gible, Honedge etc)
Everstone on whichever Pokémon has a good nature. Destiny Knot on the other. (Everstone passes the parent Pokémon's Nature onto the child. Destiny Knot passes a random 5 IV's from both parents to the child)
Breed until you have a better IV Pokémon than the ones at the day-care. Switch 'em & keep breeding until you have 5-6 IV's. Then you'll have a rare Pokémon

Foreign Ditto = Masuda Method. It's unconfirmed if it works in X/Y, but it seems like it helps.
(Masuda Method = breed with 1 or more foreign Pokémon for a higher chance of hatching a Shiny)


gl

Masuda method has been confirmed many times to work in x and y.

Link?
I haven't found proof, and I love some.

Masuda himself explained it at a conference also you can get shiny charm after completing Kalos pokedex

Shiny Charm is after National dex completion.
Oval Charm is after Kalos.

& Thanks, I'll try and find that conference. I want solid evidence.