Given the right kind of terrain, Wellington was certainly hard to beat. His record would suggest unbeatable. That said, at Quatre Bras, he was taken to the mat by Ney. I think the secret to his success is in the attention to detail, how he could always be at the right place at the right time and the fact that he was quite willing to take great personal risk to lead his troops. In short, he was a brilliant tactical minded army commander.
Napoleon I was a strategic thinker. He too could take great personal risk to win battles but gave that up after becoming Emperor. He was not above doing it late in his career though. His ability to outmaneuver his enemies is legendary. In the 1814 campaigns, he demonstrates this ability quite clearly, holding off armies several times the size of his own. In the 1815 campaign, Wellington did not know Napoleon crossed into Belgium until the French were in Charleroi. It’s actually really hard to over state just how good of an Army commander Napoleon was.
So who is better? Well we are at Olympic levels of competition here. The difference between the two men in terms of ability is pretty small. Either would do in a pinch for different reasons. If you want a campaign to close quickly, you want Napoleon. If you want to keep your army fighting, go with Wellington.
"Nearly all men can stand adversity, but if you want to test a man's character, give him power."