Ghetsis in BW also has the advantage of coming right after the battle with N. He catches you off guard. Granted, I remember beating him the first time I tried, though. Actually, I think I had more trouble with his Elektross than I did with Hydreigon.
In the end, most of my team is underleveled and the two highest leveled Pokemon I have, Magnezone and Gardevoir, get outsped and KO'ed by Cyrus's Gyarados.
I didn't have a lot of trouble against Ghestis. I caught Reshiram and used a mix of him and Haxorus to beat his Hydreigon. The rest was taken out easily.