Considering Beast Ganon(TP) and Moblin Ganon are entirely different, it wouldn't even matter anyway. It could just be FSA Ganon(who is apparently an entirely different one or something) and justify it that way.
Kind of like with Zelda/Sheik, or Samus/Zero Suit Samus.
I honestly don't think the horse fits as well as his current Brawl-style moveset. I think Beast Ganon works perfectly. However, if they use a different version of Ganondorf, then changing his Final Smash feels more logical. Right now, it fits what he does(which to be honest, he steals the plot of TP and gives you an epic battle). In Brawl, he actually was important to the overall main plot(and stole some of the glory from Bowser too!). He also isn't all that cunning in TP, so using one of the Ganon forms that clearly is more physical than tactical makes some sense.
Ganon, imo, feels like he'd word great as a heavy but tactical character. I don't know if they have any intention of giving us a different Ganondorf as is, but his stats do fit his design too. He's not severely fast by any means in TP, being way more physical. While it's true he has a horse, he's also the flattest he's ever been... much like his version of Ganon this time.
Anyway, I feel Ganon works better as a heavy weapons/magic user, almost akin to like an Ike/Zelda fusion of sorts(albeit with way more differences). I do see the point about having Ganon and Ganondorf have more unique stats, as that's the case with the other Zelda series counterparts. Ganon can be faster, as shown in his Puppet variation in WW and he's not terribly slow in OOT either, plus the teleport spam in ALttP and just him in general are hardly slow by design. I mean, more Mario speed, if anything(although to be fair, Donkey Kong and Bowser aren't even that slow either. They're actually pretty mobile, somewhat more than freaking Zelda too. Only Ganondorf in 4 is severely slow to the point of ridiculousness. To be fair, though, his battle style fits and he's basically a tank at times. You can just slowly walk through attacks and kick them right off the screen. Doesn't do enough in competitive play, but it does fit his brutal design in TP).