Okay this has been on my mind a little lately and a YouTube comment gave me an idea. I'm making this post to gauge interest, I know it's been more than two years now and hype for the game has died down a bit. Here's the rundown

Sunset takes Cadance's role as Celes.
Cadance takes Zecora's role as Banon.
Not sure who replaces Sunset in the Rachel role? Maybe Flash Magnus, have a story where he's a war hero Flash looked up to?
Include a hand wave that Sunset defected to the Empire because Celestia refused to teach her Fire magic. The Empire infused her a different kind of magic (Ice).
Keep the opera plot the same. We'll just say Sunset is dressed up like Cadance for the show.
Not sure what the Phoenix/Sunshimmer Magicite becomes. Anyone know G1 ponies renown for healing prowess, or pegasus known for courage? Note this is dependant on who replaces Rachel too, since the parallels have to make sense, so I'm up for ideas on Rachel replacements, too.

In terms of gameplay, Twilight is made the "unicorn-leaning alicorn" (most significant alicorn equipment is only available after that reveal). Celestia's stats shift to "pegasus-leaning alicorn". Twilight's exclusive "Magic Crown" Relic that lets her use alicorn equipment stays the same but we switch it to Sunset. This will be a nerf to Celestia's magical potential, but on the other hand Cadance was also a natural magic user and was the pegasus-leaning alicorn, so there you go.

The party would thus be:
Unicorns: Sunset, Rarity, Sweetie Belle, Trixie
Pegasi: Flash, Rainbow, Fluttershy, Scootaloo
Earth ponies: Applejack, Pinkie Pie, Apple Bloom
Alicorns: Twilight (unicorn), Celestia (pegasus), Luna (earth pony)
Magic: Twilight (Bolt), Celestia (Fire), Sunset (Ice)

I can make it work for gameplay balance. I can make it work for story. I'll need new graphics but that is a minor thing.

So, there's the million dollar question - shall I make Filly Fantasy VI 3.0 with Sunset Shimmer replacing Cadance?

I'd keep it as is, just makes sense to have the "lost love" set up for Flash with Sunset and in the world of Filly (Final) Fantasy VI it just seems that is the way to go.

However, if you eventually do a 3.0, for other reasons, then I can see making this change at that time, I'll likely just get the newest one as well as I already have the other 2, one benefit to having multiple versions is people can play the one they want.

I wouldn't really be opposed to it and it does seem like a good character set up. Though Flash Magnus replacing Rachel feels kinda weak.

Would Cadance also replace Duncan?

6510824
Yes. Her conferring power to Luna makes a lot more sense than Zecora teaching her a special attack.

6510760
I like the idea, although I feel that redoing the story for that is a tad extreme.

6511321
Well i would have to, Cadance and Sunset are very different characters

I almost wanna be a bit of a jerk and say to have Sunset and Flash switch places, but that doesn't seem really workable either.

How about leaving Cadence as the pegasus alicorn and having Celestia as the alicorn alicorn. As for what that would mean (for Celestia), well I'm not sure, but the totality doesn't have to be the sum of the parts. I can't remember the fic where I remember this from, but there were four types of magic, earth pony, pegasus, unicorn and of course, alicorn, as in alicorns by their very nature have access to special magic different from the other tribes.
Also, zebras could be considered an alternate earth pony tribe with access to different secrets that Zecora, being a powerful resistance leader, has access to. Cadence was originally a pegasus (as far as the books' canon goes I guess), her deep relations with the crystal empire and pegasus weather magic make ice a fitting element for her.
As for Sunset Shimmer, I also agree that it would be a shame for her to stay dead, perhaps she could be revived? Like in one of those weird General Leo hacks (not that she has to take his place). And it could a choice between the character or the magicite, where she learns the magic of phoenix naturally along with other special features that make the choice a real heavy one, not just emotionally but gameplay wise.
Anyway stuff to think about.

6511632
No, a 15th playable character isn't fully possible.

I'm already in the middle of redoing my LP dang it!!!!
But seriously, I personally prefer the balance the way it is. I'm not opposed to Sunset being included or anything though. Its up to you really. Its a bit annoying on my part as far as Let's Playing goes since my LP would thus be rendered obsolete to a certain degree again, but that is an irrelevant factor in regards to how you proceed with updating or not updating your game.

6512301
I know, I'm sorry :p You made me think of it again!

I haven't decided either way. I'm pondering it. There's still all the Phoenix symbolism and associated dead friend plot for Flash that don't line up. And the Ice magic thing.

6512567
Celestia get's ice magic? Either that or you could move it to Rarity and give Sunset Lore.

6512584
I'd sooner give Celestia lore, as an alicorn for greater magical potential, and Rarity gets Summon for her Esper bond. Catch with that though is dispersing Blue Magic to enemies earlier in the game and by their nature Blue Spells are pretty strong, tier 2 and up in power.

Hmmm... So how about Starlight Glimmer instead of Sunset (or Cadence), the whole Ice thing suits her, she has a redemption arc AND she's a powerful magician who absorbed others' magic, the only problem is that she has no connection to Flash, 'twould be shipping indeed. Even with different dialogue it's hard to ignore the romantic overtones of the Celes-Locke dynamic.

There's the possibility of making a fire Celes with Sunset. You could give Celestia gravity (could start early with the weaker demi) and meltdown (at a higher level), seems more sun themed than fire, it might change early boss battles and such. At the same time it would mean giving ice to Rarity, Sweetie Belle or Luna. The only time Celes' ice magic is relevant is when she goes against Kefka in the magitek facility and teleports him away, I don't know if that can be interpreted as stuff melting from her fire or if the color the screen takes can be changed (for Sunset doing the same thing).

As for the Rachel thing, how about Spitfire? Maybe he has a thing for the hotheaded ones it would be reasonable to assume both are military. I did find a "Sundance" from G1 in the wiki. If Spitfire is taking the place of Darill, you can always have Lightning Dust instead. She and Rainbow function well as rivals.

I have one more idea, but this one's too crazy. Twlight takes the place of Strago (lore master) and Sunset becomes Terra. Rarity makes sense as Relm (specially in the theatrics and sketching department), I guess they could be fellow unicorns escaping the stigma of magic. And that would mean Starlight as Celes (as shown above). Sadly, it would leave the CMC incomplete. Instead of Twilight becoming an alicorn it would be Sunset becoming a demon (and learning to control it for additional strength to help others, which is a lot like Terra's arc). It sounds like a completely different game, although, we have a more poignant character struggle there. It also matches Terra going crazy and looking inhuman.

6512588
Too powerful? Simple. Default ability is Meltdown. Other than Scoot, you have no way of defending against it until you get to the Empire anyway. Any other powerful spells you learn later than that like normal. Don't necessarily need to spread much blue magic other than stuff that isn't stupidly powerful so White Wind, Stone that is no longer default, maybe some of the level spells. That should suffice until after the Empire.