My least favourite Civ to play with is probably India. I haven't played with every Civ yet, but he was definitely my least favorite. Sadly, I can't really tell why I didn't like it. It could possibly be that I played a extremely tall game, but going a bit wider could be better. However, that would actually be counter-intuitive with its UA...
I have a special place in my heart for France. I absolutely despise playing against them. If I know he's close to me, I immediately focus on military to go and wipe him off the world. If he's at the other side of the world, I will bribe his neighbors, as long as he goes down as soon as possible.