There is a difference between hardest to find and hardest to catch...
Still, the roaming legendaries from G/S/C and FR/LG easily take the prize of hardest to catch: not only do they change their locations randomly (as opposed to moving to adjacent locations like the others), but they have Roar to negate trap moves/abilities (IIRC, Suicune in FR/LG is an exception to that) and in FR/LG, if they use Roar to end the battle, you lose them PERMANENTLY.
most people will just master ball legendaries though.
I suppose that proves my point, then? :P I mean, if players don't bother and go straight for the Master Ball, isn't this evidence of how hard to catch they are?
people used the masterball on GSC heracross. the masterball can be easily cloned in that game, though, but still.
Feebas is the hardest to find, with a possible Honorable Mention to Munchlax... but you could breed Munchlax from a guaranteed encounter in FRLG, with an incense that... at least wasn't random, I know that.
Worst to catch? The FRLG legendary dogs.
No clue that they're there, roaming legendaries with all that entails, and you either have to let them flee or deal with the potential that you could lose them forever.