Things that don't make sense (v2)

Why didn't the Reapers hide beyond the Omega 4 relay like the Collectors?

Or some planet(s) in some distant star system.

No need to retreat all the way out to dark space. Such a trek is pointless and silly.

What would the hostility stem from? All they have to do is lie dormant and whatever organics come into contact with them will become slaves.

They're just big strange looking ships. That's what everyone will think.

If Sovereign never revealed himself, never uttered a word in ME1, how many players let alone ingame characters would have figured out that he's a Reaper?

Also, at least according to Vigil's speculations, the reapers recharge during their invasion and hibernate in between, not the other way round.

I think the Omega 4 Relay thing is a good point. I'd say maybe the area (with black holes and everything) is too volatile to stay there for too long but then, if the collectors are the protheans, that would indicate that they could stay there for 50.000 years, so the reapers should be able to do the same thing.

So yea, good point. For that matter, even if they had to stay in dark space, why not have a second secret relay as a backup to the Citadel? There should be nothing preventing them from having a back door.

I have to say that after ME1, I was fully expecting the reapers to have a decent backup plan. After all, Vigil's tale that they are trapped in dark space is again just speculation. It would have made much more sense for the Citadel Realy to just be their preferred method of entry (as it has obvious advantages to come in right at the center of galactic power) but that if that failed for whatever reason, they'd just go for plan B and wouldn't take 3 years to fly in manually.

All that said, I think asking these kinds of questions is a bit like the "Why didn't the eagles just fly Frodo to Mount Doom in the first place?" question. It's an issue that just didn't happen in the story and was never addressed. That doesn't mean that it invalidates the plot. You could always come up with answers for those kinds of "alternative plot" ideas and why they didn't happen. For the eagles, Tolkien might just say that probably the Ringwraiths or other evil creatures posed too much of an aerial defense screen around Mordor for them to have a good chance to get through. Equivalently, if you ask Drew and Mac our questions here, they might just come up with something that wasn't in the story so far (just like our deliberations here were not) and it would be perfectly legitimate for them to do so. So I like to refrain from alternative scenarios like that for the most part.

Wasn't the backup relay the Alpha Relay?  It still seemed to take two years to get to it but that's like an eyeblink for the Reapers.  I think the bigger problem was that the Reapers needed control of the Citadel because that was what was used to control the entire mass relay system.  Admittedly, the Reapers probably win even if they never control all the relays - they're just too powerful - but this seemed to be the issue.

I bigger problem I see around all of this speculation is the idea that everyone is instantly indoctrinated as soon as they are near a Reaper.  Nothing supports this.  Saren was indoctrinated because he was spending all of his time inside Sovereign.  Even then, he had a lot of autonomy and in the end was potentially able to resist enough to kill himself.  It just shows that even indoctrination isn't necessarily an all or nothing proposition.  People can resist it.

I would say there's another Citadel like space station in darkspace. It most likely has a bunch of sub-stations orbiting around it housing many workers to maintain them. The reapers return from the harvest, attach themselves to these sub-stations via an umbilical cord so that whatever information they have is downloaded and resources to use to keep the station powered. During this time the workers give each reaper the once over. Change the tires, change the oil, get a new paint job and maybe even repair any dents or scratches the reapers may have suffered.

As far as them hiding in the galactic core? Because the omega 4 relay didn't exist until ME2 existed.

What about Sovereign flying to the Citadel and parking itself without attacking? Most likely the Citadel forces would be put on alert. Try to make contact. They most likely believe there could be other ships arriving and this one is waiting for them. The Citadel brings in reinforcements. After many attempts to communicate with the ship, they open fire. Sovereign would either return fire or realize it doesn't have the firepower to repel the Citadel fleets. So it retreats back to wherever it came from. Because of that, Citadel forces will have a larger presence while they figure out what that ship was and who was flying it. And try to find out if there's more like it in the galaxy.

He could park outside the Citadel. In the system but far enough away so as to not get CSec riled up. People traveling by investigate and take the ship for themselves. They eventually become enthralled. Sovereigns will be done.

He could hang out just about anywhere and people will try to capitalize on a seemingly abandoned capital ship. Indoctrination makes it too easy. It doesn't have to be fast either. What's 10 or more years to a Reaper?

This only works if you ignore the overall goal of the Reapers, which we learn about from the Leviathan.  If Sovereign parked somewhere, sure, it'll indoctrinate people over time.  The goal, however, isn't indoctrination.  The goal is the find a solution to the organic/synthetic problem.  Simply sitting around and indoctrinating people would bring them no closer to the goal.  They're actually testing all the races in the MW.  Whatever you think of the ending, we know that a solution deemed satisfactory to the Catalyst/Intelligence could be arrived at depending on your choices throughout the game.  However, had a solution not been found, the Reapers were more than willing to convert the "strongest" (conjecture on my part, since it's never stated) species of a cycle into a new Reaper.  Turns out we can Destroy the Reapers, leading to a potential rise of a new war with synthetics down the road.  If Control is chosen, we can enforce the peace through military race the same way the Reapers could have done all along (y'know, prevent extermination of organic species through force rather than kill them all to preserve them).

In the end, I'm just saying the indoctrination has never been the true goal of the Reapers.  It's just a tool they use to end a cycle, but even events going on at the end of the cycle could lead to the solution they seek.  Hence, if they do it too quickly they screw up the experiment.

I doubt that. The ship is just sitting there. Posing no threat. No signs of life on board. What would be the point of destroying it? What threat does an abandoned ship pose?

If its abandoned, how did it get there? Who put it there? What happened to the crew? There was nothing in that area the other day. How do I know its not there waiting for other ships to start an attack? Its a ship that has never been seen before. There has been no reports from anyone that have seen a ship like that. When I fire at it and its destroyed, maybe it will have answers explaining why it was there and who the crew was?

I know you're wanting them to so it would give Sovereign the opportunity to indoctrinate anyone onboard. How long would it take to indoctrinate them? Even if that does happen, it wouldn't be long before someone figures out that some are acting different from what they normally do. They would tell no one to go near it and likely destroy the ship

Or another way is to send drones into the ship instead of people.

True. I would destroy the ship since its possible it could be sending out a signal to other ships of its location. If others do show up, at least there would be one less ship to deal with.

Reality is that what Sovereign did has ALWAYS worked. Why change what works? Also, cycles are not the solution. The Leviathan and the Catalyst both make it clear that the cycles are an experiment, not a solution. Hence, indoctrinating people too quickly ruins the experiment.