For me, the hardest are Dunsparce & Kabuto.
The swarm for Dunsparce never happened, I have tried it everyday for 3 months.
Meanwhile, I have digged nearly 100 fossils, but only one is for Kabuto.
Other pokemons that are hard include.
Beldium(lots of hours & balls)
Munchlax(lots of days & honeys)
I hope I can meet Dunspare as soon as possible, and finish my collection.