This whole Palutena business makes me think that customs were inadvertently a bad thing for character design progress, in that they became a sort of hotspot for innovation. Since we have, for some reason, decided that we never want to see customs in tournaments again, all of these neat ideas were wasted, and we're left with relatively conservative changes to characters that needed drastic overhauls. Let's use Ganon as an example ("Wow, he's talking about Ganon again, what a surprise.")
Ganon's weight doesn't help him because he still has poor survivability in all directions except up. This is a problem for many heavyweights; these characters tend to have poor recoveries and jumps, which are the things that really count in making a character hard to kill. Ganon's issues in this area have been well-documented since Melee. His recovery is garbage; we knew it, and the developers knew it. Enter Wizard's Dropkick. Suddenly, Ganon can cover horizontal distances decently, helping him recover and actually use his weight to his advantage (to say nothing of what Dropkick does for the rest of Ganon's game). But the developers don't want to alienate character loyalists. This is the reason that Ganon hasn't been revamped in the first place. So, rather than having to choose between keeping Wizard's Foot or changing it to Dropkick, the customs system lets us have it both ways. If you like pain, you can still play original Ganon, who is defaulted for familiarity. If you like pain slightly less, you can play Ganon with recovery options (I've gone this whole paragraph without mentioning Dark Fists, another clear upgrade to an abysmal default). But you can't play Custom Ganon in tournaments, so only the conservative default design is visible.
You can see this conservatism of default design in Palutena as well. She has customs that are incredibly distinct, and her default seems to exist as a bland, simple, beginner's version of the character, with a counter and a reflector rather than her more unique customs. This should be all upside, as you could play simple Palutena is you want to, and delve into her customs if you want to optimize her or adapt her to your style. But again, these design choices are invisible to us.
Customs have allowed for interesting design on the more and character level, but are shockingly poorly implemented when it comes to actually setting them and unlocking them (I think the fact that Palutena has her customs unlocked by default is actually a huge point in her favor.). I find it truly bizarre that you can't just mess with them on the CSS. It really does kill me that one of the best innovations in Smash 4 has had its back broken by poor menu design.
More troubling is the fact that the community just does not seems to like customs, and to be specific, the Against side is more passionate about the issue than the For side, from what I've seen. Players who want customs might consider this a +1 of some arbitrary enjoyment unit for their experience of the game; players against customs seem to consider it a -100 to their enjoyment. Pro-customs players just aren't willing to skip tournaments and force TOs to cater to them, and so customs have more or less fallen off the map. The best thing, I think, the developers could do to challenge this would be to make customs legal in 1v1 For Glory with random strangers, so that the community gets used to them. As it is, all their work seems to have been for nothing, and we're left with a more conservative game than we might otherwise like, in terms of character changes.
TL;DR: Customs became a space where developers could try different things to help out flawed characters, while avoiding player alienation that might result from outright replacing old moves. Because we ignore customs, we're left with many characters whose flaws were not at all addressed in their default configurations.
