But vayne was a good threat towards them. He was a threat towards their entire COUNTRY. You're looking at the villain from too much of a "villain appears shoots them with lightning and runs off laughing" type of villain. Vayne isnt like that. He works behind the scenes and manipulates those with power to get his way. He's a man looking for war and conquest, he doesnt have time to stalk and follow the rag-tag group on his own. Hell, if he showed up in person a lot I'd see that as out of character. A villain doesn't need a bunch of boss-fights to be good.

And I know you were joking, but I still see it as a tasteless and unfunny joke.

Vaan was made to be the relate-able rebellious teenage lead. For some he succeeded, for others he failed. While his character design was questionable, I found his character endearing. He was extremely naive, and I think they played it well. He let his emotions carry him too much at first, but he grew a LOT as the game went on. So, hell, even if we want to consider him the lead he isn't that bad at all.
As it stands, I consider Ashe the lead. She does much of the leading, and she is extremely essential to the plot as well. Her character was handled beautifully, and the ONLY criticism I have for her is the mini-skirt which I found to be quite silly.