Judging by that ending it didn't seem like there was much of a difference in IQ between the two... in fact I would say Vergil made the dumb choice there.
Plus it was Dante who came up with the idea to use Lilith as bait exchange. If Dante is motivated he is just as smart as Vergil but he is rarely as motivated as Vergil.
Lillith is kind of a moot point, you have to remember that Vergil didn't know about Lillith's importance. He couldn't formulate that plan without the variable that only Dante knew. And the ending, eh I wouldn't say Vergil was dumb or smart in that case. That was just two people seeing the world through a different lens.