I think it's less that Haki is superior to Devil Fruits, so much as Devil Fruits are susceptible to Haki. I think, ultimately, the story is going to reveal that you need BOTH Haki and Devil Fruits to achieve the highest level in this world. You're going to need both if you want to find the One Piece.
And, honestly, I think eventually we're going to get a reveal of a Third Power System in the One Piece World. We're just missing one part of our "Weapon Triangle".
In the video game Fire Emblem, there's a weapon triangle. A rock-papers-scissor mechanic. Where Swords beat Axes, Axes beat Lances, and Lances beat Swords. I think by the end of One Piece, we'll end up something similar with Devil Fruits, Haki, and this Third System.
Right now, Haki beats Devil Fruits. But, chances are, this hypothetical Third System can beat Haki. And possibly only a "Awakened" Devil Fruit can beat the Third System.
And chances are we've already seen this Third System. This is probably in some way related to the Gorosei and God's Knight's Abyss powers.
It's also probably all related to that quote from Gol D Roger from Chapter 100. "There are three things in this world that cannot be stopped. Inherited Will. A man's dream. And the flow of time. As long as people hunger for freedom, these three things will exist."
"Inherited Will" is related to Haki. It's the willpower to see something through and produced by the strength of body. Armament Haki increases the strength of your body, Observation Haki increases the strength of your eyes, and Conqueror's Haki...is a bit of a outlier, but maybe we could say it overwhelms your opponent's strength with your own greater strength.
"Dreams" are related to Devil Fruits. They are manifestations of a person's desires and are produced by the spirit within a person's soul.
"The Flow of Time" or "The Ebb and Flow of the Ages" should, therefore, probably be related to this Third System and possibly the power of the mind. Thus completing the trinity of "mind, body, and soul".
We've seen that the Gorosei have some sort of "Telepathic" ability amongst themselves. A "mind power" that allows them to communicate with each other islands away. "Telekinetic" abilities would also explain how Saturn was able to freeze people in place with a look on Egghead (Chapter 1094-1095). It may have been the result of his Gyuki power, or it could have been this Third System. Even "Teleportation" via the summoning circles, is classicly seen as a psychic power in Japan. (See: Akira.) The fact that the Gorosei and God's Knights all seem to have muted or reserved emotions also kind of feels like a hint that they're using "mind" powers. They are the type of people who are literally "plotting from the shadows".
The Abyss powers also are likely tied to whatever happened in the Underworld, if the mining operation shown in the Chapter 1138 Mural is any indication. And given how Gunko thinks that whatever is supposed to make the World disappear is inevitable, it's likely also connected to "repeating history" or "fate" in some way. Knowledge of what happened during the Void Century may make them think that history repeating itself again is inevitable, thus again linking this to a "mind" power with it being tied to "forbidden knowledge". At the very least, the Gorosei being effectively immortal does feel like it gives a link to "the flow of time".
And notably, Luffy was pretty easily able to damage the Gorosei on Egghead in his Nika form. He couldn't cause any lasting damage, but at the same time, they couldn't really do much to him, either. This does kind of hint that a Awakened Devil Fruit could be immune to the Abyss powers, at least once you "embrace your dream" enough. It's possible that the secret to stopping the regeneration powers is somehow tied to embracing your dreams, or inspiring a dream in the opponent?
So, it's not so much that Haki beats Devil Fruits, in every situation. I think it's likely that we just don't have a complete picture of how all the power systems in the One Piece World interact with each other.
Luffy's crew is "designed" the way it is for a reason. Luffy's crew is like a "balanced" JRPG party in a video game. He has a few Devil Fruit Users (your Black Mages). He has a few non-Devil Fruit warriors with strong Haki (your Tanks, or Warriors). There are a handful of very smart or clever people who could probably adapt to using a "mind" power like possibly the Abyss power (Nami, Usopp, Jinbe, Robin, or Chopper would ALL make for interesting candidates for wielding Abyss or Abyss-like powers). And all of them have really strong dreams.
Other crews aren't as "balanced" in this way as the Strawhats are. Blackbeard has gone for using ALL Devil Fruit Users, making him very susceptible to Haki. (But, it WOULD make sense if he was stacking his team so he could take out someone like Imu.) Shanks has NO Devil Fruit Users, making him very susceptible to the Abyss, in theory. (But, that would make sense, if Shanks is mostly worried about dealing with Blackbeard.) Imu, the Gorosei, and the God's Knights are all-in on the Abyss powers, meaning they're susceptible to something like the Nika Fruit. (But, it might have made sense to do that in the past, if they had to fight a bunch of strong Haki-users like Joyboy).
It's likely the strongest opponents in the Final War will be the ones who can use all three of these abilities together. Imu can most likely do that. Blackbeard will likely get to that level. And Luffy will most likely get there, too, eventually. Even though, Luffy's "mind" is his weakest quality.
The overall lesson here is likely to be that it's a good idea to have friends who can do things that you can't. If all your friends are just like you, then they won't be able to help you out if you get into a jam. But, if you have a bunch of friends who all think differently than you, or can do things you can't, then there's really not much that can take you all down when you all work together. (Chapter 90)
Haki is a important ability. But, it's not likely the "strongest" ability. Chances are, there are things out there can can beat Haki-users. And that's why it'll be important to have a diverse crew, if you really want to find the One Piece.