Again, it's tauros. I don't think it matters whether the pokemon is a shiny or not, because you can simply breed them with ditto (and as for legendaries, soft reset) thus evening the chances. However, the exception to this is Latias/Latios, which you have to go to all the trouble of finding and in any case, you can't soft reset like you can with other legendaries.
So,
Hardest to find: RBY Tauros
Hardest shiny to find: Latias/Latios
That's what I think ^-^;