Since Ganondorf and Captain Falcon play in completely different ways it's hard to distinguish which one is better based on moveset alone. But Ganondorf has, by far, the better moveset. His neutral A is actually useful, and Dair has much more possibilities and is easier to land than Captain Falcon's Dair. Utilt is cool for edgeguarding, but is useless otherwise. USmash, on the other hand, is better than Captain Falcon's, even if it comes out slow. Ganondorf has overall much more power on his aerials, and the most important ones, Nair and Uair, aren't that much slower than Captain Falcon's.
While Captain Falcon wins in terms of speed, you can still see his special moves coming from a mile away, so their increased speed doesn't do much. And of course, his taunts are epic win, but Ganondorf's aren't lame like Samus.
It's sad that Captain Falcon lost a lot in the transition to Brawl (hitstun, an easily sweetspotted KoJ, etc.). I guess it depends on who you are as to how good you think either is.