I think it's telling that the canonical reason Prometheans look like they were designed by an idiot is that they were designed by an idiot. Senile, insane, senseless. I mean, the Didact melted down his Promethean super-soldiers into fragile tin cans, on the supposition that he was making them immune to the Flood.

In a more general sense, I think the good folks at 343i have a terrible problem with objectivity. They can't distinguish their intent from the execution, so they are blindsided when the stories they tell fall flat.
Let's break it down:

-Intent: Promethean Knights are tragic enemies, not mindless robot monsters.

Execution: Mindless robot monsters.
Scarab has said it better than I can. But seriously, what the Hell us up with the skulls?

-Intent: Watchers are a part of the Promethean Knight, sort of a splinter of the soul.

Execution: They split off from the Knight in some sort of weird techno-organic birth, with a burst of synthetic amniotic fluid to complete the effect. But no indication is given that this is a process of mitosis, rather than yet another teleportation animation.

We often encounter Knights without Watchers. We also encounter lone Watchers (or even swarms of them) without Knights. If they're supposed to be the same entity, they should be sticking close to each other to the point where the player can easily tell which Watcher belongs to which Knight.
Also, change up the tactics when one of them gets killed, like Hunters do.

Intent: The Watcher chattering sound is when they see you, and are reporting you back to their Knight.

Execution: The only thing that happens when a Watcher is spying on you is that they make that little chattering noise. Knights don't change their tactics, and neither do Crawlers.

-Intent: Promethean weapons transform and adjust themselves to fit the user.

Execution: They. Don't. Transform.
A Promethean weapon lying on the ground is almost exactly the same lying on the ground as it is when you or a Knight holds it. When activated, they just extend some floaty bits and fire up the Tron lines.
Oh, and the break-action shotgun still has the pistol grip when a Knight is holding it, which is about as useful as tits on a Sangheili.

In all likelihood, the transformation was toned down so players could easily recognize weapons when they see them lying on the ground. Which is a really crappy excuse.

-Intent: The Didact is the Chief's nemesis.

Execution: The Didact tries to be the Chief's nemesis. And is a lesser character because of it.
In order for a nemesis to work, the protagonist and the antagonist have to have roughly equal levels of power, they have to be working at cross-purposes, and they have to be familiar.

That's what makes Shepard and Saren nemeses. They're both Spectres who are building a coalition to reach a goal, they're trying to stop each other, and they each try to convert the other on multiple occasions.

That's also what makes Kai Leng so hilarious. He wants to be the nemesis to the big bad Shepard, but he's just a weaboo hitman who has to move heaven and Earth to be considered more than a nuisance. Shepard has bigger things to worry about.

So, the Chief is a supersoldier cobbled together by a backwater species. The Didact is a general who was in power at the height of Forerunner civilization, ensconced in his own fortress-world. The Didact should have been a demigod, but then the Chief couldn't have reasonably fought him.

Which is why the Didact doesn't do anything to kill the Chief. And that makes him a Bond villain, not a nemesis.

In conclusion, when you're writing a story, it's easy to make the connections because you know all the important details. But as a writer, your job is to communicate and justify that intent. If you don't have enough objectivity to evaluate how well you've communicated that intent, your story is going to fall flat.