I will put both literally hardest/rarest, and as well as my personal ones that are the hardest/rarest. (This does not include glitch pokemon cause I really think they should not count.....Mew probably would be my answer for hardest/rarest, depending).
Literal (Hardest) - Metagross B/W:
Can be caught in wild but only in tall grass, has a 5% chance of being found, is around Lv. 55-60 and have a catch rate of 3 (legendary pokemon catch rate)......yea not fun.
Literal (Rarest) - Feebas D/P:
If I am not mistaken they lowered the amount of squares to find this blasted pokemon in wild, increase the amount of squares to search for it, and shuffle it every day......this is why GameShark/AR was my best friend for this pokemon alone.
Personal (Hardest) - any roaming legendary:
Hate with a passion......without a strong pokemon to trap them and no false swipe to diminish their HP to 1......it is annoying, and especially when they don't want to be in your route when you travel.
Personal (Rarest) - Feebas D/P:
See above......I swear the wasted hours...... >.<!!!!!
Recently Finished Game: Ni No Kuni (PS3), The Last Story (Wii) Current Game: Pandora's Tower (soon) (Wii), TBA (PS3), MH3U (WiiU)