Goddammit man. You brought it up again. I know my Ganondorf rework idea didn't tip you off too much, but I think a fundamental problem you have with this subject is this unwritten rule that Smash Bros characters need to be consistent through the series because "that's just how fighting games be". I don't buy it.
I know people want to say that comparing fighting games with a MOBA is fallacious, but screw it. Let me show you how hero reworks happen in Dota 2, and why almost every single hero rework in the past 3 years has been seen as a positive thing, along with the few that haven't and WHY they haven't.
Good examples:
Necrophos rework in 7.00
Viper rework in 7.07
Lich rework in 7.20
We'll start with these three.
First, Necrophos. His rework involved his main damage spell, Death Pulse, being merged with one of his two passives, Sadist, which restores health and mana slowly over time whenever Necrophos kills something. With the merged Death Pulse/Sadist, he gained a new spell called Ghost Shroud, which makes him immune to physical damage and heavily increases healing he receives for a short while, as well as slowing enemies around him.
Necrophos' goal as a hero has always been a "slow burn" style of intelligence carry hero, staying within the fight for a long period of time, healing himself and his allies while passively and actively whittling away at his enemies. Before 7.00, he had no disable to keep people within range, no way to outheal most incoming damage, as well as no way to keep up against agility carries. With Ghost Shroud, not only are these weaknesses addressed, but because he gets healing amplification (the first healing amp spell in the game mind you), he can further bolster his other spells in various ways. In short, this huge rework made him not only better against things he was bad against, but also gives him a more complete moveset.
To give a Smash equivalent example, imagine if Inkling didn't have a way to manually refill ink and it passively did it over time. Yes, she would still work, but far far less than giving a clear cut extra tool to bolster the rest of her kit.
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Viper used to have two passives as well; Nethertoxin, which gave bonus attack damage based on the enemy's missing health, was merged with his first spell, Poison Attack, causing the damage over time to increase based on missing health, rather than Viper's attack itself. Nethertoxin was then reworked to throw a pool of magic resistance corroding acid that is very spammable, and disables heroes' passive skills should they stand on top of them.
Another example of bolstering Viper's moveset, because not only does he have plenty of slows to keep enemies in the Nethertoxin pool, but his magic damage is immense, and lowering resistance means it will hurt FAR more. On top of that, he was the very first hero to naturally cause passive skill disabling in quite a long time, giving him a specific niche he never had before in the metagame. This was after years of Viper simply being mediocre in all senses as a carry. Now he is one of only two heroes that can disable passives without needing an item, and he is actually used because of it.
An equivalent in Smash would definitely be Bowser post Brawl. In terms of purpose, not many of his moves changed, but his much higher mobility allows him to actually give a unique experience and threat level he would've not had otherwise.
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Next is Lich. Being one of the least changed heroes in the entire game since the very first Dota patch ever, he got two entirely new skills, replacing his unequivocally most boring spells. Ice Armor simply gave your teammates armor, and you had to play continuous upkeep throughout the game. His other spell, Sacrifice, removed an ally creep from the game, granting him mana, and his teammates the experience from said creep. This one spell put him into a very specific bubble as a "lane winner, game loser", where he would absolutely dominate the early parts of the game, but fall off hard later on, and because of his specific niche, there was little they could do to balance him adequately without just making him useless, so they just decided to remake the hero.
Frost Shield is a temporary buff that is like Ice Armor, except it is not spammable, and has a MUCH bigger effect, as it slows enemies around the ally you cast it on, as well as damage them periodically, giving him great teamfight capability. Sinister Gaze replaced Sacrifice, and while a very simple spell where you stun and pull a single enemy towards you, it was a hard disable on a hero who didn't have a hard disable, plus, it synergizes with Chain Frost, his ultimate, by forcing an enemy to stay close together, because to stop the spell they must hit Lich, but getting close to Lich while doing it bolsters the Chain Frost to keep going. Overall, Lich is a VERY common pick now and a unique hero all the same, though his purpose as a hero has drastically changed.
Smash equivalent is definitely Link, as his Remote Bomb Rune is far more versatile and playstyle defining than his old bombs. He can continuously hold and throw it without detonating to keep enemies back, he can hit it with an arrow or boomerang to cause it to drop in a certain way, and he can still self-detonate for recovery anyway. He has been repurposed for the better, and as such he is the most successful he has ever been in the series thus far, and is a unique fighter all the same.
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To contrast, here are some bad examples and why:
Bad examples:
Io rework from 7.14
Chen rework from 7.20
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Io has historically been a problematic hero balance wise, though starting at 7.14, he's been considered as slowly rebalanced to "remove skill" playing him. The big one is the Spirits skill losing its oscillation sub-abilities, disallowing very precise movement of the spinning orbs around Io in favor of a press to go out, and another press to go in, with no manual in between to stay on. People, especially dedicated Io players, were not too happy with this. For a Smash equivalent, it is similar to taking away certain options completely without much replacement, very similar to Ultimate Bayonetta.
The reason this was overreacted was because not only was nothing actually taken away option wise, but it helped lower the skill floor of Io, a historically low winrate pub hero, just that tad bit. Plus, there was a lot of other wonky interactions with the subabilities that were not worth worrying about. In Bayonetta's case, notice how people are finally not sticking to how she lost her ceiling combos and focusing more on how well she can combo horizontally now with her much weaker UAir? It's like that.
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Chen uses creeps (Dota version of minions) to attack and help his enemies and allies. The big change is now he cannot control the stronger creeps until later on, while historically he was considered one of the strongest heroes level 1 because a strong creep is roughly equivalent to a level 1 hero in terms of potential. Now, he has more buffs, and is played more like a buffing support rather than the army building ganking support he used to be.
The reason this isn't too much of a problem, or not as much as most players would say it is is because weaker creeps still are useful, and have been buffed over the years and most Chen players barely notice this because the stronger creeps are still stronger. This is a bit of a different case because I still feel Chen needs some tweaks to become less buff oriented only, but he already got a big one in the very next major patch, 7.21, where his new buff, Divine Favor, does double its buff on creeps he controls, giving him a reason to lug creeps around again, even if they are weaker.
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These two examples were to show that it isn't the inconsistency in the character that is the problem, but very specific gripes that can be accounted for in the future without completely rolling back all changes done. But as I say, if you rework the Smash Bros fighters to either have a more defined purpose or more available options within that purpose they have, I'd call that the hallmark of a good Smash Bros fighter rework.
In conclusion, stop equating these reworks as bad because they are faithful to canon, especially when they give these characters more utility to work with, like Bowser and Link. As for Ganondorf, his rework is definitely more good/bad for those three moves replaced, but he still has disjoints he never did otherwise, so like Viper, it's giving him a little niche in terms of options by having good disjoint power.