The main thing you need to watch out for when recovering is Ganon's U-air. Reverse U-air gimps Mario pretty easily, but good DI can help you avoid this. Make sure you DI Up against his F-tilt of course.
One thing to look out for is simply punishing him for attempting to edgeguard. I've gotten quite a few gimps by simply Cape Stalling after I get past one of Ganon's failed edgeguard attempts.
D-smash can be retardedly difficult for Ganondorf to punish if he isn't prepared for it. It ducks right under his D-air, Jab, Grab, and F-tilt from what I've seen.
Mario's combos on Ganon of course are really good. D-air -> U-air -> U-air -> D-smash is about 48% on Battlefield (end the combo on a platform). U-tilt chains him to like 30% and then you can get 2 U-airs and a grab for over 60%. Heck, D-tilt can put Ganon in a tough position due to his aerial options being a little bit too slow and if he tries to punish with N-air, you get a Smash out of shield.
One Cape is all it takes to destroy Ganon's recovery. If you Cape him once, the only way he can make it back is going for the edge, so it's a free edgehog as long as you don't screw up. The other way I gimp Ganondorf a lot is by jumping into him with a U-air. If Ganon has used his midair jump when you do this, he won't make it back.
Mario's Jab outspeeds a lot of Ganon's options, so that sucks for him since you can often just do an aerial -> Jab and he can't punish it easily.
When I use Ganondorf, most of my KOs either are from F-smash or doing a reverse U-air gimp if I know Mario is trying to aim for the ledge (Mario however can Up-B early to mess Ganon up). F-smash is something to watch out for because the leanback makes it able to punish Mario's B-air really hard if you're not careful. In general my strategy in this matchup as Ganon is just to Dash Attack and Flame Choke at opportune moments to deal damage and try to juggle Mario as much as possible since Ganon's U-air is hard for Mario to challenge. Then mindgame him into a F-smash or throw him offstage and either gimp with U-air or mindgame in a Smash or an aerial when he does a ledge jump. As long as you watch out for those things, you'll probably win against Ganondorf.
If we discuss another matchup, either I want to hear more about the ICs, or talk about Peach (and yeah, where are you BO X7?).
As for Peach, I'm thinking the matchup is slightly in Mario's favor. Just slightly. Basically, Mario outcamps her (slightly) and overpowers her in KO moves (moderately). Peach's advantages like recovery and combos don't stack up enough when Mario works around those advantages decently by camping with Fireballs and out of shield options (which Mario does better than Peach, as his Up-B is better defensively, and his Up-smash is superior offensively when compared to her other options on his approaches). Mario's Up-smash and F-smash are both better KO moves than anything else Peach may have aside from a lucky Bombomb. Up-smash punishes her out of shield if she approaches with an aerial. F-smash outranges her and KOs earlier than her aerials or F-smash do IIRC.
Basically, I feel this is currently one of Mario's best matchups against a character that is ranked higher than him.