We've gone back and forth quite a bit about this, and I don't think we're going to change each other's minds, so this is the last thing I'll post about this:
I don't really agree. Saren's mentality was warped and the Reapers were still villainous, yes, but it's still built on the same principles of cutting off advanced civilizations for getting too advanced and too chaotic.
Honestly, I didn't notice any particular principles behind Reaper ideology in ME1, beyond self-interest and contempt for us squishy organics (see Sovereign's speech on Virmire; superior beings that are trying to save organics from themselves or from the universe would probably not boast about how much we suck). Sure, the Reapers want to cut civilizations off from getting too advanced, but I saw little indication that there was anything to this beyond the trivial fact that more advanced civilizations would be better able to fight them.
The series' central strength, which has always been its character writing, isn't the same as the series' core antagonist. And it's clear that both were central to the series as a whole, else they would have left the Reapers in Darkspace at the end of ME1 instead of killing and resurrecting Shepard to fight 'em.
I'm not claiming that the Reapers aren't important to the story, but what I've argued consistently is that their primary importance lies in their function as a plot device to advance the other conflicts of the story. Ultimately, everything plot-wise in DAO comes back to the Blight, but I was not expecting to have a conversation with the Archdemon at the end of DAO in which he gives me the answers to the universe. Same with ME as far as I'm concerned.
Yet you have no idea why you're going to Ilos, since the Conduit is a MacGuffin all the way until that point. All that's known is that it helps Saren's goal in bringing the Reapers back from Darkspace. The fact that it was a conjured backdoor teleportation device onto the Citadel (which bends the lore behind relays like crazy) was a plot contrivance at best, though it's still worth appreciating that the Protheans were attempting to grasp the nature of the Reapers' technology.
You'll have to forgive me here; I'm actually rather confused as to how this is supposed to contradict anything I said, so I'm going to skip it.
Malick's hit and miss with general audiences period, though, because of his focus on poetic cinematography and leisurely pacing. Not really a fair comparison, and I do think it's worth considering one of the ideas originally conceptualized by the series' initial writer, since he's the origin of this thematic infrastructure you're referring to.
I actually think it's a fairly apt comparison, seeing as it's pretty clear that the original ending, thick with religious and abstract imagery, is going for something pretty avant-garde and a bit outside the tastes of popular audiences.
They darken the skies of every world and have been successful for millions of years and countless cycles. I'm not a huge fans of conventional means since that devalues the intellectual, cultural, and industrial prowess of every single cycle beforehand.
There's only so much you can do here. At a certain point, the only way not to devalue every previous cycle is to just make it not possible to win the game. No matter what plot device you use, there will always be the question, "Why didn't the previous cycle figure out how to construct this plot device?"
Having said that, I think my proposed scenario has a neat solution to this. With only a relatively small number of Reapers, you have a clear rationale for why they shut down the relays--it allows them to overwhelm each system individually, without ever having to worry about reinforcements from anywhere else. When shutting down the relays is no longer an option after ME1, they become more vulnerable. So the plot device you need was already provided in ME1.
/night
EDIT: Fixed formatting