Whew... where to begin...
And the Reapers aren't Cthulu, they're just advanced.
Uhm... yes. They are. They are directly inspired by The Cthulhu Mythos. Soverign himself stands in for the actual Cthulhu as the one who will run off and grab his brothers when its time to throw down. He's a mind destroying space squid who induces paralyzing fear and 'cannot be understood'. Do you really need more?
Hell the Human Alliance fleet took out Sovereign at the cost of about ten ships, (hell technically speaking they only nabbed the Destiny Ascension... so one ship)
Soverign was sitting on his hands >.> only reason he grabbed the Destiny Ascension was it was the biggest ship there and it was in his way. So it was a demoralizing running slam, went straight past it and went for the Citadel. Geth had his back. The only, and I do stress, ONLY reason the humans got him was because they came in at the last second when the battle was pretty much in the final stretch, and swarmed Soverign while he was still UNABLE TO FIGHT BACK and the Geth and Citadel fleet were locking horns.
Soverign could take down a good two thirds of that fleet on his own. The reason he didn't was that wasn't his goal.
and the Quarians have oodles, and oodles of ships, add in the fact that the Turians have the largest fleet in Citadel space and suddenly a galaxy unification idea doesn't seem so half baked
Okay, so we're multiplying the battle of the Citadel by a good deal here. Soverign would have taken a good chunk of those forces with him, but victory wasn't likely. Even outnumbered, he was a terrible force. But there are hundreds or thousands of others like him... even the unified Quarians, Turians, Krogans, Salarians, Humans, and the Rachni and Geth if you went that way, are still looking at a long, bloody, hopeless battle. The only difference made is they may take a dozen or so down with them.
There's a reason the Reapers cut galactic communication
Your right, there is. It's a very simple one, one employed by machines in fiction since forever. You know what it is? You ready for this? Logic. Not fear of losses... your wiping out a galaxy. Its logical to cripple it first. The culling is organized the way it is because its damned smart and makes an unbelievably complex and messy job much more manageable.
There is no reason to assume that all the reapers are as powerful as Sovereign either.
Not all, but they've been doing this how long? Even with the culling going smoothly, they face opposition. Disorganized, crippled, doomed opposition, but the fact they prepared for the event of the culling plan not going ahead means they planned for the rest of that scenario. They knew there was a chance the killswitch wouldn't get pressed. They prepared for that, with Soverign. They ARE prepared for a war, because they need to be. They are machines.
The theory stands though, if you can kill one, you can kill 'em all.
If you can gang up on one thats solving a rubiks cube and chained to a chair, then yes, you could take out another with extreme numbers on your side. Hell, snag two, or three. Sure, that one just wiped out a few dozen of your ships, and some of those were some real hard ass models. But unless you outnumber the entire Reaper population by a hundred fold, all your doing is making them cull harder next cycle.