In 3.0.2 I felt that Ganon could hold his own against Captain Falcon and that the matchup was around even, however now that the game engine has been tuned a little closer to Melee's, I'm starting to see that Falcon does hold an advantage over Ganon, even with the new tools we've been given.
I play against a lot of Captain Falcons. I stomp the ones that are bad, and get absolutely wrecked by the ones that are good. Falcon's Shffl Nair literally combos into itself on Ganon at low % to the point where there's literally nothing else I can do besides buffer a roll when I'm getting nair spammed.
Falcon's Up-throw->Knee is essentially guaranteed above 50% regardless of DI. If the Falcon is good, he'll be able to get the knee on reaction to your DI no matter what.
DI'ing in on any of Falcon's combos will lead to a lot of followups, and outward DI on the ledge can lead to some dirty edgeguards. Your combo DI in this matchup needs to constantly be on point if you want to compete against top Falcon mains.
Some things we can do well against Falcon is keep him in the air with Rising Nairs, like we can do vs all fast fallers. His tech roll is also ass, so if you can force tech-chases then you have a good chance at being able to punish on reaction. Float helps bait getup attacks, and allows you to put yourself near Falcon without committing - but Falcon can travel anywhere across the stage extremely quickly so empty floating can get you killed easily.
Another strategy I've heard mentioned is space yourself at the edge of Falcon's shffl Nair range, then use your own AC Nairs on reaction to punish his. I have yet to test this, but I know from experience that Falcon's nair out-prioritizes almost all of Ganon's aerials. I'll try out this strategy and post back what I think about it soon.
The way I usually deal with Falcon in the neutral is to DD at the edge of his Shffl Nair range and try to bait him to approach with SH Bair Wavelands, or Full Hop double bairs. I play an extremely aggressive Ganondorf usually, so this matchup is one of my worst ones. I'm friends with a few other Ganon mains who have experienced more tournament success than I have, and their playstyles are much more patient and punish heavy than mine, so maybe my problems are on more of a fundamental level.
TL;DR - Ganon vs Falcon is 40/60 in Falcon's favor - IMO.
Here's a video of me playing against Champaign's top Melee player - MattR
Here's a video (from the same tourney) of my buddy Demia playing against Matt R
Note: These videos were taken around the time 3.5 was released so neither Demia or myself were too experienced with floating. I also had not begun incorporating SH Bair Wavelands into my game yet, only FH Double Bairs (which I was constantly being punished for lol). I also did not use Nair OOS nearly as much as I do now.