I'd say all the double battle gym leaders are the hardest. I'm relatively new to pokemon (only ever played Gen1 and 2), so I can't do synergy yet.
I'm fine at filling my team with full coverage against everything, so in single battles, I just switch out whichever mon is the rock to their scissor. I just need to figure out which rocks to bring. In double battles, those scissors are always accompanied by a paper to counter my rock, and I have to adjust the whole thinking process.
That said, I have a tendency to use a lot of steel pokemons, so Charlotte just double pain.