Alright. So I just did my own playthrough of Leviathan. I gleemed a few thoughts from the final conversation:
1/ For a race so hell-bent on being secretive, they sure do spill the beans the moment Shepard gets close to them. Almost eager to discuss their history, infact. That alone is suspitious.
2/ "The Intelligence." Leviathan never states that its an AI, or even a machine. Shepard says that, and Leviathan merely doesn't comment on whether or not that's correct. Combined with the blatant lies of ignorance on the Crucible (yes, that pause and focus in on the sidewards glance was very obvious), its evident that Leviathan isn't happy with Shepard knowing the full truth.
3/ Leviathans. Supposedly they are the basis for the basic Sovereign class design. However, since they state Harbinger is the first, its weird that Harbinger doesn't actually share the number of limbs they have - lacking the central limb. Also, their overall shape is actually somewhat different to Reapers. Not sure what to think of that, but it is odd.
4/ How they were defeated. They gloss over the details. Quite how they are defeated when they never state "The Intelligence" as being a weapon, and the fact they control the other races, isn't stated. Merely that they were suprised. With what, exactly? The Intelligence apperently didn't even have Reapers to overthrow them with yet.
5/ Ease of convincing otherwise. They go from "we're doing nothing, and you are own slave" to "okay, we'll fight" from a very short speech. Sure, they might be afraid that the Reapers now know where they are hiding - but...
a/ They can apperently instant-kill Reapers in close proximity. Kill that one, or any others that come close, and they are safe still. b/ If they can't leave that planet, then what is protecting them whether they fight or not? c/ If they can leave that planet, then they can hide somewhere else without much trouble surely?
Overall, just... Yeah. Leviathans can't be trusted, not in the slightest. The fact they blantantly show Shepard can be controlled, and have his/her memories used to construct an illusion just about says it all.
I think it's safe to say that Harbinger played them all for fools.
In other words when Harbinger was created it was to slove the Leviathans problem right. Organic thralls vs the Synthetics, now the only way I can see the AI, well Harbinger gather allies to help him over through the Leviathans were the Synthetics.
Harbinger hacked the Synthetics of his cycle, and over time it was building the Citadel for the Leviathans to show them that they are inpower over the galaxy. It explains why it's so huge.
Now when Harbinger was building the Citadel with the help of his inslaved Synthetics, it was setting up a trap that would kill so many Leviathans, that it would let Harbinger have his new body he oh so wanted.
So when the Citadel was being created Harbinger's enslaved Synthetics were building his Reaper body. Then after the Citadel was complete along with Harbinger new body, Harbinger sprung his trap.
When the Leviathan government were on the Citadel Harbinger gave the Keepers the Thrall race that was genetical rewriten in secrete to close the Citadel. As that Happened communications were shut down, and Harbinger's Synthetics attacked the Leviathans, and the Keepers activated the Citadel defencess. After the Leviathans were killed Harbinger orderd the Synthetics to gather the dead Leviathans and turn them into Genetic material.
After a few days or weeks Harbinger was reborn. Now you see Harbinger only had the power to Indoctrinated the Synthetics, but with the Leviathans powers to Control Organics, it profected their powers into Indoctrination. So Harbinger used all the Synthetics, and Thrall races including the non thrall races to kill the Leviathans.
Once the Leviathans were defeated, Harbinger knew that the next cycle, and even the one after that would try to stop him, and his new Reapers, so he created the Crucible a false weapon that is only to waste the Galaxys materials into one huge object.
That could be why the Reapers managed not to die those first few cycles and the ones before that. Only it was later that a race caught onto the Crucible being a trap, the Protheans believe it or not.
If you think about it. The Protheans didn't create the Crucible, nor did the cycle after that, so who could have built the Crucible? The Reapers, well Harbinger.