I was thinking about it more, and I am no longer convinced doc is better than ganon.
Ganon is slow, but not much slower than doc. Other than move speed, ganon's attacks are relatively quick. His moves are all the same speed as falcon's, though his aerials have more lag. Between his slower jump speed and the higher landing lag, he is slowest between SHFFLs, but he has one of the best ranges in the game to make up for it.
Ganon has the best throws in the game and is able to combo into a kill move on nearly every character. This is generally one of the reasons people rank doc so high, his chaingrabs and throw->fair. But ganon has more chaingrabs than any other character.
At the edge ganon is beast too. His edge-to-stage recovery is unmatched. He has more invincible frames after a ledgedash than almost any character, a strong wavedash and a huge roll. Between the two distance extremes of ledgedash roll and stand-up, it is impossible to cover everything he could do. Flip sides, he has one of the best edgeguards after the top tiers. Even tho this is 2012, most people still can't meteor cancel ganon's dair due to the awkward timing. He has an easy to do invincible ledge stall and a ton of options for preventing the opponent to get back to the stage.
On stage, ganon has some surprisingly tricky movement. His double jump tricks alone are worth making this section. Keep in mind that uair has a lot of range going forward at the early parts of the hitbox and can hit a standing fox on the way up. SH uair DJ fair. SH uair DJ platformdash. SH bair DJ dair (the ol' kage high/low). Ganon can jump out of fullhop dair and fairs the same way. Combine all his strong interrupts with his long waveland and high range, and you have a character that can manipulate space very efficiently.
His glaring weakness is his recovery. He can make good distance, but the linear nature of it makes it difficult. If ganon can grab edge with a jump, his isn't in too much danger, but beyond that he is in trouble. Kage has figured out a few tricks tho, such as delaying the downb. In order to go off stage and hit ganon after the downb, most characters have to be moving to where the downb would take ganon by anticipation not by reaction. Downb is a true spike, so it can have a similar affect as falco's side b in terms of reversing an edgeguard. Albeit much slower, the threat alone is valuable. While ganon's recovery is worse than many other usable character's recoveries, it still has its merits.
Match-up wise, doc and ganon both lose to all the top tiers, though doc may do better if it matters. Ganon does better against the high tier characters: Peach, Marth and Falcon having even matchups with all of them. Doc loses to marth and falcon, im not sure how he does vs peach (definitely not better than even). Going down the tier list, ganon does much better than doc, too. Ganon has more chaingrabs than sheik
tl;dr, I think ganon is better than doc in nearly every category. I think ganon's recovery is better, his zoning tools are stronger, his edgeguard is as good or better, his edge recovery is incomparably better, and his combos are as good or better. What doc has going for him are pills and cape as well as his body size.