Balance is indeed the name of the project, but diversity isn't up for being sacrificed. Sacrificing diversity is just fake balance anyway. I'll explain this point a little more in-depth so we don't have misconceptions.
In any fighting game, there is a natural rift between diversity and balance. The whole idea of balance is that assorted game units (in the case of a game like smash bros, that means mostly characters... though stages too to an extent) are as close to each other in overall value as possible. Diversity means those same game units are as different from each other as possible. It's obvious how these two conflict. When things are similar, they naturally drift toward being balanced as they have the same principles governing them. When things are different, they naturally drift toward imbalanced because, as Hyrus put it, ROCK beats SCISSORS. It may even be that in this game PAPER beats SCISSORS too; maybe SCISSORS just really sucks on a fundamental level.
However, the best balanced fighting games are the ones that optimize not just balance on the raw level but the product of balance and diversity. Street Fighter 1 is not considered a serious fighting game despite being the most balanced fighter of all time; having more than one selectable moveset is generally considered more important than all selectable characters being equal in value. We could go for fake balance easily enough; we just fix the bad things about every character. Make Ganon faster and safer while making Sonic more powerful at scoring KOs, that sort of thing. Maybe we don't have to go all the way; maybe we just turn Ganon into a second Donkey Kong and Sonic into a second Fox while letting Donkey Kong and Fox still be pretty different from each other. However, it's all the same bad. Why even have Ganondorf and Sonic in the game if they are just going to be very similar to Donkey Kong and Fox?
What that means for this project is that, yes, we're committed to making every character viable, and yes that includes characters like Ganondorf. However, what makes Ganon unique is simply not up for sacrifice. Making Ganondorf similar to other characters is not a lot different from removing him from the game. In the end, this makes the balancing job harder, and since perfect balance is impossible unless we make all characters exactly the same and thus any project can only attempt to approach it, this probably means our final approach toward balance will be slightly sub-optimal since we deliberately deny ourselves many things that could help us balance. That's okay. The game is better this way.
Ganondorf is also seriously not that bad right now, just saying.
And as per what makes a character viable, you have to think on a higher level. Ultimately, a character's viability can be measured by 36 numbers, and those are matchup numbers. If a character has all matchups that are close to even and not basically all of them negative, they're viable. There are other viable matchup spreads than just that model too, but let's not get into the nitty gritty. Within a matchup, what determines how good or bad it is is best measured primarily by risk-reward style analysis. Each character has a variety of potential strategies they could employ, and those all carry assorted levels of risk and promise assorted levels of reward. The opposing character can employ their own strategies as attempted counters and they are likewise. If one character has a low risk high reward answer to almost everything the other character can do with the remainder of what the other character can do not being really, really awesome, then the matchup is probably skewed. However, matchups like high risk high reward versus low risk low reward are not necessarily skewed; those are all just a function of the particular risks and particular rewards. Things on a lower level than that, such as power, speed, or range, are useful tools, but they are ultimately below the radar of balance in the same way things like "has a frame 1 invincible move" or "has a full screen projectile" are. The lower level than that is things like "has a jab that hits in under 3 frames" or "has a forward smash that does over 20% damage"; it's just getting into more specific things that are too narrow to provide insight. They matter, but they matter because they influence higher level things, not as independent entities. They are adjusted, but they're adjusted in a big-picture kind of way, not for their own sake.
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Samus's bombs should blow up on contact IMO.
Samus's bombs are already pretty good. The way she uses them in Balanced Brawl is how they seemed like they should always work in standard Brawl. She lays a bomb while retreating at a medium range, and if the opponent closes in, the bomb covers the space. Even if they hit Samus, the bomb does enough damage that it's probably a favorable trade made better by how Samus is a character that has amazing survivability and thus more often benefits from trading damage than most characters. Exploding on contact would be the sort of change we generally try to avoid, and it's just unnecessary because her bombs are already a good move, probably better as an actual attack than they ever have been in previous smash games even where they did explode on contact.