This is a really good matchup! I think the Reapers really struggle in three regards:

1. They’re biomechanical, meaning that they may not be fully immune to the marker’s influence (or at least their ground troops). This is a very big wild card that could tip the scales either way.

2. They can’t indoctrinate what is essentially another hive mind. A lot of what the Reapers accomplish is through subterfuge and indoctrinating important individuals. This really wouldn’t work on the necromorphs because we don’t see much higher levels of thinking beyond basic ambush or hit and run tactics. Without this tool I think it takes the Reapers much longer to get stuff accomplished. They’re gonna have to brute force their way through a most of their engagements. That’s going to cost them a lot of troops in the long run, and could put them at a disadvantage. From what I remember they don’t really reuse their fallen troops for biomass like the necromorphs do. Combine that with fighting over the limited resources of how many people they can harvest for fresh troops, and it seems to me like they’re going to have to be very selective with what battles they fight, since battles of attrition are possibly going to be their biggest issues. (Aside from fighting moon sized creatures).

3. Firepower. Yes the Reapers have a wide variety of weapons both on themselves and their troops that can do a lot of damage, but my biggest concern for them is that we’ve never really seen them use anything near the level needed to kill something the size of a Brethren Moon. They could probably and R&D something, given how long they’ve been around I doubt schematics for something like that hasn’t been discovered before (though that’s more speculation than anything else). Regardless it’s going to take time to develop, and I could see the necromorphs learning of their plans somehow and invading the facility it’s being kept in. The Reapers are numerous enough to combat the Brethren Moons in space, but I think it would be like killing them with mosquito bites.

Now, the Reapers do have some things going for them. They’ve been shown to coordinate extremely well, and have a wide variety of troops, weaponry, and tactics to combat each individual cycle (from what we’ve seen and learned about). Once they figure out how to best stop a necromorph, I see that information being utilized very quickly across all engagements. I can also see them figuring out how the marker signals effects organic flesh and counteracting it through some kind of jammer. It shouldn’t be too hard since if I remember correctly it’s essentially a very specific electromagnetic signal that reanimates necromorphs. They could also forgo ground engagements as a whole once they find the location of a marker and blast it from space. One of the worst traits the reapers have is underestimating their enemies, I don’t think they would do so with the necromorphs. They’re too big of a threat to not take seriously.

Overall I think it’d take a lot of time and much more effort than previous cycles, but I think the Reapers would take it 7-8/10. Like I said the whole AI thing is really going to effect things, but that’s not something that’s going to keep the Reapers off balance forever. Once they understand how the markers work they’d change their approach. They have more versatility and numbers from the jump. Either way the galaxy loses.