ME 1 also establishes that the Reapers built the Mass Effect relays - the galaxy-spanning network around which galactic civilization is based. This isn't replicable, they are the only means of long distance space travel in the main mass effect series, up until ME2 no mass effect relay had ever been damaged and they are believed to be indestructible, and in ME2 it's revealed that although they can be destroyed, their destruction will release energy on par with a supernova. ME 1 also has Sovereign and the Geth bypass the known Mass Effect network to lay siege directly to the heart of galactic civilization. Granted, we see how this works, it's a backdoor they built into the system. But given they built the system, who nobody else can understand well enough to replicate, I think this still counts.
You're not getting it. Relays are very advanced technology that is presently outside the grasp of the citadel races, but it is still just that, technology (and it's not that far out of their reach. The Protheans managed, and per Aethyta the asari could have tried to build their own relays). Lovecraftian horror is not about the unknown for now or the tricky to figure out, it's about the
unknowable, the kind of knowledge that simply cannot align with mortal understanding of the universe and that drives men made if they start to grasp at the real truth of the universe.
If relays were, say, something like a Stargate and jumped ships from point to point instantly and no one had any clue how because the laws of physics insistent that nothing like that is possible, and the last few people to try and reconcile the relays to known physics all went nuts and started ranting about cycles of history larger than the aeons or whatever, then yes, that would be lovecrafian. But instead, people go "It's like a mass accelerator, but bigger".
In all three games, we repeatedly see people think that they can use Reapers or Reaper tech safely, that they can put safety measures in place to mitigate indoctrination, and it never works. There's never an "oh, turns out it was just EMF or nanobots" moment where they actually figure it out and can actually stop it happening. I don't think having characters that think they know what they're doing is un-Lovecraftian, as long as those characters turn out to be wrong in dramatic fashion, which they do in Mass Effect.
That's actually wrong, people can use reaper tech safely. The Thanix cannon is reaper tech. EDI is reaper tech. It's
difficult and
dangerous to reverse engineer and tamper with reaper tech, but it is not impossible.
More important, you are again missing the point of lovecraft. "I thought I knew what I was doing but didn't" isn't lovecraftian, the point of lovecraft isn't that we make mistakes and misunderstand the nature of the mythos on first encounter, it's that the mythos proves that we understood
nothing in the first place, that our fundamental conception of reality is wrong. Reapers do not work like, reapers are poorly understand and dangerous, but they are knowable in the end.
People in ME don't understand exactly how indoctrination works or how to block or control it, but they understand how it works conceptually, and can even manipulate it to some extant (Lawson cracked at least parts of it, to the point even the reapers were concerned enough to run in and stop him). That is anti-Lovecraftian.
Reproduction is hardly un-Lovecraftian as a motivation either. It's base, but Lovecraftian Horrors are frequently base. The cycle being part of the life-cycle of the Reapers doesn't make them less Lovecraftian.
I remind you, you said that prior to ME3, reapers were
"beyond comprehension," terrible and inexplicable beings "without beginning or end,"
ME2 has people comprehending the reapers well enough to sell bits of them to the player as shiny new guns, and you witness the beginning of a new reaper, on top of witnessing the end of one in both ME1 and 2.
Literally the only thing that suggests the reapers are anything but big evil squid robots with advanced technology is that one conversation you have with sovereign, who is obviously lying to you even within the context of ME1, let alone ME2. And that conversation itself undermines the idea of it being lovecraftian, because you get under Sovereign's skin.
You cannot annoy a Lovecraftian god, they are so far beyond mortal concerns we're like ants to them. An individual ant might annoy you, might sting you for a bit and cause you minor pain, but it's still so far beneath you that even if it does attract your notice, you will simply squash it and move on. You won't care about that individual ant, or expend any real effort trying to kill it, or try to deduce it's motives or have a conversation with it where you explain how insignificant it is. You just step on it and be done.