Anyway I'm gonna give thoughts on the match up. This is gonna be long btw, like, way longer than it needs to be.
Strength:
First up is the considerable gap in strength. Bowser is superior to beings that use Power Stars (Which at least generate 9.88 foe) putting him at the higher end of Large Star level. While Ganon is closer to the lower end of the tier. Even if we were to assume Ganon has the power of a supernova he'd still be around 10 times weaker and less durable than Bowser. It would take repeated chip damage for Ganon to match just 1 punch from Bowser.
Skill:
In terms of fighting skill both have shown skill with different weapons (Ganon with swords and tridents, Bowser with hammer and magical wands), and both are highly skilled with magic. However in the end I'd give Ganon the edge in skill due to his final battles in The Wind Waker and Twilight Princess where he matched Link, who is a highky skilled swordfighter.
Powers and abilities:
Before I get into this there's one point I want to address, the wish granting abilities of the Star Rod and Triforce. I've seen plenty of people on the Internet say "Ganon via wishes on the Triforce" or "Bowser wishes his opponent away with the Star Rod". Personally I only go by what wishes they've been said and shown to grant. I'm not going to say Ganon can erase Bowser with a wish, because the Triforce hasn't shown the ability to erase people, nor will I say Bowser will erase Ganon, because the Star Rod has never shown that ability. As wish granting items both the Star Rod and Triforce are prone to NLF and I personally think it's best to only use whats been shown with their wish granting.
Now we move to their abilities. They share a lot of powers (Such as elemental manipulation, teleportation, duplication, and summoning just to name few), and they also have abilities the other doesn't (Bowser has stuff like spatial manipulation and time travel, Ganon has stuff like invisibility and death manipulation). However overall I'll have to give Bowser the edge in this category, for starters Bowser resists a lot of Ganons magic. Death Manipulation? Resisted. Elemental Manipulation? Resisted. Being pulled into the Dark World which transmutes people? Resisted. Power Nullfication? Resisted. Sent to the gap between dimensions? Teleports out. Whereas Ganon doesn't really resist any of Bowsers abilities. While Ganon does have resistance to sealing (One of Bowsers abilities), it's not very good resistance seeing how he's been sealed away multiple times and needs years to break out of them, so Bowser can more than likely seal him away. Also Ganon has no counter for Bowsers "Endless Staircase" trick, what's to stop Bowser from keeping Ganon away with spatial manipulation while spanning transmutation or sealing spells? Now Bowser doesn't resist all of Ganons magic (Like mind control) but he resists a decent chunk of it, limiting Ganons options.
Now Ganon has low-godly regen,
but it has drawbacks that make it far from perfect. And Bowser has infinite self-resurrection, whenever he dies he pops back to life seconds later at peak condition (Basically low-godly regen for all intents and purposes). Neither Bowser nor Ganon has the ability to kill the other. Bowser can't destroy souls, and while Ganon does have soul manipulation, he hasn't shown anything overly impressive with it, plus I think Bowser displayed resistance to soul manipulation in Super Paper Mario but don't quote me on that. However, Bowsers resurrection happens almost instantly as shown in the Thousand Year Door, whereas Ganon either needs a few weeks to construct an ideal body, or go insane by creating a new body instantly.
Also slightly off topic but why does the Triforce grant resistance to mind control, it can't be from Link resisting Agahnim since he never even used or even attempted his mind control on anyone else besides the castles soldiers. I'm asking because Bowser apparently has mind control and I want to know if Ganon would actually resist that
Bowser has transmutation, he turned the toads into stone and plants in the original Super Mario Brothers, and turned a Koopa into a frog in Mario Party 2. Ganon has no counter for this, and Bowser has shown he's willing to use this (He used this on just a regular Koopa out of anger, so it's very likely he'd do the same to someone much more powerful than a Koopa). I'd also like to point out that Bowser has power nullification of his own as shown in the Thousand Year Door:
Conclusion: Between the large advantage in strength, resisting quite a few of Ganons abilities or having a counter for them, along with stuff like transmutation spatial manipulation which compliments his already superior range, I think Bowser wins 7 times out of 10. In the event Bowser dies he just pops back to life seconds later, whereas Ganon losses his intellect advance if forced to regenerate. Not saying this a stomp in Bowsers favour or Ganon has no chance whatsoever, but to me, Bowser is more likely to be the victor.
Ganon:
•Superior Intellect (Unless forced to regen)
•Can seal Bowser
•Can mind control Bowser
•Invisibility
Bowser:
•Far greater durability and strength
•Infinite Resurrection
•Spatial Manipulation (Can make it so none of Ganons attacks or magic can reach him)
•Superior Range
•Warping time and space
•Can seal Ganon
•Transmutation
•Resists Ganons Elemental Manipulation, Death Manipulation, Power Nullification, Poison Manipulation, Dark World BFR
•Power Nullification
Thats my needlessly long thoughts on the battle. Feel free to disagree and argue against it.