Okay, here's my analysis.
Ganondorf as a Character
Strengths: Powerful, good range, great edge guard, good aerial game, Flame Choke (good for mixing up approaches, chasing, and comboing)
Weaknesses: Poor mobility, predictable recovery, useless Neutral-B
Place in the Metagame: Low-Mid Tier. I believe Ganondorf is viable, but it's undeniable that he is on the lower end of the spectrum. Ganondorf punishes mistakes hard, but is generally forced to play the opponent's game and wait for them to make a mistake. Ganondorf is especially punishing if the opponent is off-stage, but this is kind of counterbalanced by how abysmal Ganon himself can handle being off-stage. He has more recovery mix-ups than in Melee, but he still remains amazingly easy to edge guard. Overall, Ganon has a few great strengths and even more glaring weaknesses.
Room for Improvement
Neutral-B: The obvious one. This move is essentially only useful if there is a broken shield or a sleeping Jigglypuff. Even in those situations, a fully charged Smash attack or even an up-tilt will generally get the job done. My personal opinion is that the move should be scrapped entirely. If it was given super armor, it could find some small use in edge guarding, but Ganon already has plenty of options in that department.
My hope would be a projectile, just because that would give him options and be cool, but problems with articles, if my understanding is correct, would make it difficult/impossible to implement.
Either way, just about anything would be better than what he has now.
Recovery: I like the suggestion to give Ganon less lag when he successfully grabs off of Up-B, but I feel being able to jump out of it would be too much. Same for jumping out of side-B, but that seems slightly more reasonable.
I would like to see his Side-B snap to the edge more quickly. It's silly to see Ganon smear his face against the wall and then get punished for trying to mix-up the recovery. Mainly though, it just looks silly.
Armor: I oppose the idea of strapping super armor onto Ganondorf. For one, it is a feature that should be used sparingly and only when it makes sense. Bowser needs it, and he's a spiky armored behemoth. Squirtle goes into his shell and gets it, which makes enough sense.
Adding armor onto any of Ganon's existing moves, in my mind, wouldn't make a lot of sense. At the very least no move comes to mind that looks like Ganon enters a protected stance. Secondly, spacing is a big part of Ganon's game, and I fear that armor undermines that. That's more of a personal opinion, but that's my take.
Crazy Ideas: Replace Neutral-B with: A projectile of some sort, dark energy wave thing from before boss battle of OoT, or really just about anything.
Explosion of dark energy on bair to differentiate the attack from Falcon and more fully detail the disjointed hitbox.
Keep the fair animation the same.
New dair animation would be fine, but not the Brawl one.