They aren't using them because they're jankly balanced. So, if we balance them...
There are a few reasons why I stopped using customs in normal play (aside from Miis).
#1: My local tournament scene doesn't allow them. If I'm used to playing against characters with customs, I would be at a disadvantage playing against, say, a Bowser that has a command grab instead of a slash.
#2: One of my main reasons for using customs in the first place was to buff weaker characters. If this project turns out to be successful, then customs won't be needed.
#3: Customs makes starting a game slightly longer, since I have to select customs for each character whenever I switch character.
#4: A lot of the customs are annoying to play against, such as Wii Fit Trainer's Jumbo Hoop or Donkey Kong's Kong Cyclone.
Some comments on these:
#1: This doesn't apply to non-tournament players, or tournament players that play in a region that allows customs. Furthermore, one could argue that playing this patch also puts one at a disadvantage in tournaments. That's true, although if we stick to some data buffs for the lower tiers, then I don't think the change will be all that significant. Changing moves, like customs do, is more significant.
#2: It's possible some characters (such as Ganondorf) would benefit more from customs being allowed than from whatever buffs they get here. Still, if this project works as intended, then customs won't be needed.
#3: One could argue that this is a pretty minor detail, and it is. Still, it's worth mentioning.
#4: You could just stick to non-annoying customs.
So, what happens if we do end up balancing customs? Do we balance the character with the assumption that they will use customs? In that case, characters with good customs will get fewer buffs than they should, and people using the standard set will be worse off compared to if we didn't balance customs at all. If we balance the characters with the assumption that they will use the standard set, but we also buff the customs, then those characters may end up overpowered with the customs. So perhaps it would be best to just balance the standard set and let people chose custom moves if they want, but those moves won't be buffed. This has the additional advantage in that it saves time.
Also, we shouldn't feel a strong need to have a character end up being high tier. Chances are characters like Little Mac and Ganondorf won't be high tier due to their glaring flaws in their design. A high tier Ganondorf would probably not be very fun to play against, for instance. I'm strongly against turning anyone's custom moves into standard.
As for Miis, I don't know. Perhaps it would be best to just focus on their main moves and skip the Specials altogether, since more tournaments allow customs for Miis than customs for all characters, but not all tournaments allow customs for Miis. For me personally it doesn't matter that much, since my local tournament just allows Guest 1111, which basically means that no one plays Miis, so I'd just be using Miis for fun.