The rarest wild encounter is encountering Surskit on Route 102. According to Bulbapedia, if you walk in the tall grass on Route 102, there is a 1% chance of encountering a Surskit.
Hmm.. There is no such Pokèmon, other than:
1) Pokèmon that cannot actually be found around Hoenn
2) DexNav exclusive Pokèmon, which is pretty rare, such as Growlthe for example
Other than legendaries, of course. (Maybe I'm wrong, but eh.)