I've had several close calls, but that was just me using strategies or something.
For me, it would probably be Ghetsis in Black, his Pokemon kept KO'ing my team, forcing me to use Revive after Revive (and maybe even a Hyper Potion here and there) and it was down to just his Seismitoad and my Samurott. I manage to defeat him in the end but oh god that Hydreigon was such a rough thing, and I had trouble hitting it super-effectively. N would have to come in second thanks to the fact he leads with Reshiram/Zekrom and also has a powerful Archeops that I struggled against a lot thanks to the fact it was fast and hit hard.
Iris in Black 2 was almost as hard, as I had very little that could counter her Pokemon and I was surprised that after her Haxorus hit my Lucario with a Dragon Dance-boosted Earthquake, he did not get one-hit KO'd and I managed to defeat her. But oh god Earthquake caught me off guard.