The Rachni wars were the Leviathans, trying to recruit a species to battle the Reapers. As far as I remember.
Do you have a source for this? I was actually wondering about this in another thread.
Sovereign had indoctrinated Saren and Benezia. Between the two of them they should have managed to sneak someone onto the Citadel and execute the relay procedure. Saren was a Spectre, he had all clearances and could have simply walked in while the Council wasn't in session. No one needed the Conduit at all, everyone involved had access to the front door, there was no need to find a back door. Neither would Sovereign have needed the Geth.
It's possible the proceedure for opening the Citadel was too complex for two organics to handle. It might've tried to forcibly input the data into their minds, but that would decrease their effectiveness, as we are told indoctrination does.
Even assuming that Sovereign needed to dock with the Citadel to accomplish its goals, it could have pretended to be an ancient prothean vessel which was found by Saren. Again, who's going to say no to the top Spectre if he wants to dock his ship so everyone's scientists can go aboard and study it? They would have welcomed him with open arms, because they were all eager to know more and were greedy for more new tech.
I am sure that there are several other ways to accomplish its goals without firing a single shot.
Ships don't dock right at the Presidium, at the council chamber. As fascinating as the Protheans are, the Council would've raised an eyebrow at that request. And if it was a Prothean ship, why bring it to the Citadel to study it? Given what we know of the asari and their beacon shenanigans, they would've insisted that it be studied at Thessia. Refusing would've also raised some eyebrows.
Sovereign fucked up badly on Eden Prime. First of all, it wasn't necessary to show itself, it could have sent Geth ships instead. Secondly, transforming the colonists and scientists into husks had no purpose and hinted at something else.
Saren's experiments with the Rachni queen and the Krogan clones made no sense either. What would those be used for? The Reapers didn't need them. Was Sovereign just humouring Saren? Was it a hobby?
The rachni queen was the only living thing that remembered the location of the Mu relay which led to Ilos, which is where the Conduit was. The krogan facility was to keep the krogan loyal. Perhaps it was also to keep Saren loyal as in his mind he was beginning the work of perfecting life, or whatever he was on about.
Speaking of hobbies, what was up with Harbinger's little project? Collectors? Building a human Reaper? Why? What for?
Meh, get the ball rolling? Humans had proven themselves a threat. A human Reaper would've done wonders in terms of understanding our strengths and weaknesses as well as a huge blow to morale for us. Was it strictly necessary? No. But since Harbinger could do it, a better question would be why not?
Last but not least, the Reapers are a flawed creation and they do not make sense. Every Reaper is a gestalt AI which consists of millions of advanced, sentient programs. What do they need the genetic material of the dead races for? If the Reapers are storage devices for the history, culture, technology and knowledge of the races they wiped out, why would they risk themselves in combat? Doesn't that go against their directives of preserving organic life in Reaper form?
The organic component heightens their processing power above those of comperable machines (not that there are any) somehow. Either it has bases in actual organic computing (which is a thing) or it's mostly technobabble. But still along the principle of "strengths of both, weaknesses of neither". I could get more into it but I gotta go.
The Thorian was creepy and could have been more... except I kind of killed it in ME1. So there was no role for it to play in ME3. 
Like it'd be the first time something has turned out to be "not quite dead". Or whoever said that was the only one?
Aria is so a villain. She's a warlord, the ruler of Omega, the leader of all gang leaders. How is she not a villain? If you asked her, she'd tell you she is. 
But she's on our side.
P.S. I love Mass Effect but the writers didn't create good antagonists. The entire story only makes sense in hindsight, from the perspective of Commander Shepard. Just one example: On the first mission to Eden Prime you're accompanied by a Spectre named Nihlus who wants to evalute your skills because you are considered to become the first human Spectre. The problem is... Eden Prime was not planned to be a combat mission. If Sovereign and the Geth hadn't attacked, then the Normandy would have landed on a peaceful, agricultural planet, Shepard would have signed for the Prothean Beacon and then they would have flown to the Citadel. The only thing Nihlus could have judged would have been Shepard's prowess with paperwork.
And let's just forget about how the Council publically announces and broadcasts galaxywide the identity of their newest secret agent. Who becomes a celebrity that endorses stores on the Citadel. Yeah...
That wasn't to be the only mission Shepard was judged on. He would be evaluated over a period of time, on a number of different missions. Sad that Nihlus bought it. He was kinda cool.