Alright cool, glad I could help! Yeah I suppose that's fair. Although those highlights tend to be about as thick as the black outlines are, it might be impossible to do the secondary light source consistently for some sprites anyway.
Nice, so do the kids all have to share the same subpalette of 15+1? a nice last touch, would be having the lower half of their faces be the more light pink/peach like in the art.
For Larry's hair, it could have more contrast and a cyan-ish highlight if that's possible.
And for Ludwig's hair, you're now doing the secondary light source thing on the lower part of it whereas before (and in the original) it's shaded darker there as if lit from above.
I think I prefer the star on Morton's face being larger like you did before honestly, it doesn't quite register as a star shape now.
Lemmy's mouth seems wrong, it's not supposed to be elongated out from his face like that, it's supposed to be wide and just a bit longer for the upper half. It now looks a bit like a duck.
https://vignette.wikia.nocookie.net/villains/images/7/74/Lemmy_SSBU.png/revision/latest?cb=20181206161616
https://pbs.twimg.com/profile_images/827959740214964225/36nko_Cz_400x400.jpg
Wendy and the others look great to me, nice work on the red glasses.
Edit:
Could you also share your .pal file for yychr? I assume the SMW one mentioned in the guide is different.
I'm not really sure what a subpalette is. Ludwig and Larry are the only ones to share a palette, They all have 16 colors. Unfortunately, I don't think making their muzzles lighter will be an option. Perhaps if I change the grey parts of their palettes into a light flesh color it could work, i'll have to see when I get the ability to edit palettes again.
Speaking of, I had the same thought about Ludwig and Larry's hair. But like I said earlier, I'm not doing palette edits until I get the build script DarkSamus has been working on. I can however make a mock-up by altering the colors in YYCHR. I'll post that later down the line. I haven't done much tweaking to Ludwig's original sprite so the light colors on the bottom slipped by me.
Lemmy is an odd one. I'm trying not to reference modern Mario artwork here, but it's not like there's any good official artwork of the Koopalings in profile, so I think it's okay to take a peek at modern Lemmy art... that being said, there's not a lot of consistency here. Like, this was made for Mario Kart 8.
But so was this.

And I don't even know what to say about this.

More than anything, I want to avoid referencing the 3D models since they are, in my opinion, the most boring and rigid versions of the characters to look at. But on top of that, they don't match even some of the modern 2D art. Larry's nose in 3D is really big and rounded like Bowser Jr, lacking the little button like bump where his nose should be.
With all that said, I've taken your suggestion and applied it to Lemmy because I wasn't really satisfied with him. He just has such an oddly shaped face compared to the rest of the Koopalings... but I did realize he's actually pretty similar to the King of Water Land's Kappa form, who also went through a similar change ( his picture in the OP is outdated, waiting till I can get the Dog and the Seal into the game before updating it )
Here's how they look now.

Looking at Ludwig again, maybe I will take another whack at him. He might look better with his head tilted a little more down but that hair is a doozy to work with since it takes up all of my real-estate for that sprite.
Ah, that tutorial I shared is actually meant just for Super Mario World. They have the advantage of having Lunar Magic to extract pal files and other things. I have no idea how to obtain .pal files from other games. What I actually have to do is make save states in ZSNES when what I want to edit is on the screen. Best to re-name them immediately after you make them so you know what they are and don't accidentally over write them.
I can share the save states I have, but keep in mind, if you test them out in the game, a few things might not look the same since I've done palette editing work on some things ( specifically Triclyde in world 1 of SMB2, Player sprites in SMB2, Larry, Wendy, Roy, and Ludwig in SMB3 ) Here's all my save states so far:
https://mega.nz/#F!WeQhyIiQ!1PZR31_M3sMMKSfcTjbJeA It might appear to not have everything but some of the palettes are a bit more global and you can use any of the palettes from their respective games to edit them. Although in the case of SMB1 and TLL it's good to keep in mind some things change color depending on their environment.