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Sovereign needed Saren to find the Conduit because Sovereign simply isn't powerful enough to take on the entire Citadel Fleet...not to mention the various respective Citadel race fleets that were merely a hop skip and jump away (i.e. like Earth's Fifth Fleet). So he couldn't just attack the station. That and the station closes its arms when under attack, so Sovereign would have attacked the station only to be left outside of it and inevitably destroyed. Reapers are powerful, but not invincible. In fact, their main advantage is their indoctrination and harvesting abilities. As individual ships, they are actually pretty weak. Sovereign is the most powerful Reaper in the series, and even he isn't powerful enough to take on the Citadel Fleet by himself.
Now, why couldn't Saren just use his Spectre status to open up the Citadel for good ol Sovereign? Well early on Shepard's investigation ends Saren's Spectre status. Saren didn't intend for anyone else to be able to read the Prothean beacon on Eden Prime, so when Shepard was able to do so, it put a dent in his plans (which is why he was so pissed when Shepard was discovered to have seen the beacon). Maybe Saren orginally did intend to just walk into the Citadel and start the Reaper invasion, but Shepard screwed up Saren's plans pretty badly once his Spectre status was revoked. So Saren couldn't just walk into the Citadel and access the restricted Citadel defenses. I mean, even with the Citadel Invasion at the end of the game, it took Saren awhile to actually program the Citadel to permit Sovereign to enter. I don't think anyone is just going to let him screw with the defense systems. Spectres still have some restrictions. Especially considering that Saren was under investigation.
Oh and Spectres typically work alone. Saren just walking in to the Citadel Council Chamber with an army of Asari Commandos is definitely going to cause a stir. I understand what you mean though and it does come across as a slight plot hole, but their are some reasonable explanations for why Saren couldn't just walk into the Citadel. The wild goose chase for the Conduit was all because their wasn't a direct link to Ilos. Saren and Shepard had to follow the pieces left by the Protheans. Since the Protheans had thousands of planets under their Empire, it could have been any planet even though IIos was known to a select few (i.e. like Liara).
1) The Reapers leave Sovereign behind to monitor the next cycle after the Protheans have been wiped out.
2) The last of the Protheans on Ilos finish their custom-built mass relay, using the Citadel itself as the sister relay.
3) Those last protheans take the relay (the conduit) to the citadel and sabotage as much as they can that is tied to Reaper control, and mostly succeed.
4) There are two important elements of sabotage that matter: (a) Remote access to Citadel hardware by Reapers not in physical interface with the Citadel, and (b) cutting off the connection between Reapers and the Keepers. The Reapers have no trouble control another thrall race from as far away as dark space -- the Collectors. But they can no longer control the keepers, which default to their old orders of maintaining the citadel
5) Sovereign deems it time to begin the next harvest by the reapers, and sends the remote signal to the citadel. There is no response from the station or the keepers.
6) Sovereign realizes that the citadel has been sabotaged, and this sabotage must be investigated and repaired in-person in order to turn the dark space relay back on for the rest of the reapers; otherwise, the reapers have to travel the long way.
7) Sovereign, a bit in the dark on the exact nature of the sabotage, realizes it needs to both try a physical interface AND use loyal/indoctrinated sentient beings to check the keeper/small scale side of citadel computer interfaces. As an either-or-approach could fail to solve the problem, and would alert the Council races of some impending military threat to the citadel upon failure, a second effort would face enough resistance that could risk defeat and the death of Sovereign. Therefore, the troubleshooting effort must include both Sovereign's arrival AND a substantial ground force to take the key part(s) of the Citadel to fix the sabotage and connect dark space relay.
8) The combo of ground forces and Sovereign's presence makes it very difficult to accomplish if Sovereign goes in without a fleet. Therefore, Sovereign seeks support ships and finds willing Geth (though indoctrination and infiltration to seize other ships was the backup plan).
9) A fleet still needs a route to the Citadel. Normally, the trip to the citadel requires passing through several mass relay pairs (only somewhat displayed in-game). Moving a fleet through any of the previously-mapped AND guarded relays would give ample time to the Citadel defense fleet to prepare, mount a proper defense, or call reinforcements that arrive BEFORE the fight instead of during (ALA Humanity's 5th fleet).
10) Sovereign is then left with three options: (a) use an overwhelming fleet assembled without the Council's knowledge to barrel through a guarded path of several relays, (b) use a currently uncharted/unguarded relay path and take a moderately-sized fleet with the advantage of total surprise, (c) send the fleet in from sublight speed, taking months or even years to reach the Citadel, or (d) abandon the dark space relay effort and signal to the Reapers to invade under conventional propulsion, even if it takes years to arrive.
11) Option C is moot because it has roughly the same time-to-enact as option D but carries risks that option D doesn't. Option A might seem like an option in ME1 (the geth are not bound by any treaty and nobody has been getting a good check on their 300-years of shipyard activity, who knows how much military hardware was built up), but it is clarified in ME2 as non-viable. Sovereign only has willing geth, a fraction of the geth forces that can be estimated at-most to be 1/3 of total geth derived from geth fleet war assets and planetary codex descriptions.
12) As such, Sovereign must choose between option B or D. It decides that D is the backup plan in case B fails.
13) B requires finding the travel method the prothean's used for sabotage: the rumored conduit, the artificial relay, whose existence is proven by the sabotage and whose design intention is not a secret (Ilos itself was a successfully-kept prothean secret, but the efforts to build an artificial relay were not). This then requires investigating prothean ruins and council records for such information and clues to find the conduit and use it as a back-door to the Citadel and bypass the fleets waiting along each multi-relay path.
14) Saren proves effective in collecting existing information about the prothean efforts and finding new sites to investigate (Eden Prime, Therum, Feros, Virmire). His exact recruitment was in one of the comics.
15) Saren probably could assemble a substantial force of indoctrinated allies and smuggled geth to attempt his operation on the Citadel and check that side of things for sabotage. But if that doesn't fix the sabotage in the case that Sovereign's physical interface was required, then it's a waste and Sovereign still has to get through several relays and fleets unless using the conduit, only now the citadel defense forces are on high alert and may have geth recordings or indoctrinated prisoners to test/interrogate.
16) The Thorian provides the cipher to understand prothean beacons, Eden Prime and Virmire beacons reveal Ilos as the site of the conduit, and the Rachni Queen has knowledge of Ilos' system normal (reaper-built) relay and it's sister relay's location after it's stellar displacement (the Mu relay).
17) The whole "sovereign's shields hold up until Saren dies" thing is a contrivance not supported elsewhere. Reapers of Sovereign's class can be damaged and killed by conventional fleets, it just takes time and causes lots of casualties. Sovereign making a solo run on the Citadel, even with the conduit and surprise, faces a substantial risk of being killed before being able to both physically interface with the citadel and close the arms to protect itself from the remainder of the fleet. No dead reaper depicted in the sequels required an avatar like Saren, nor did they have such a weakness.
18) Not only Saren, but Sovereign and the geth fleet DID use the conduit. Relays are complicated machines[/spoiler]that can be programmed from proximity-jump protocols to a degree of distance and precision, with various-sized object having different values[/spoiler]. Smaller items (with less than 1/1000th the mass or size of any non-strikecraft ship) could be put directly on the Citadel, but large ships needed greater safety distance to account for drift. i.e. Poor precision for a big ship like Sovereign could jump directly into a citadel ward/arm, destroying or crippling both. It's still an unacceptable risk for Sovereign to take a closer jump.
Because 4, 10, 11, 12, 17, and 18 all require playing the sequels, they ARE plot holes for ME1 release 3 years before ME2. This is made more problematic by several other points being reached by logical inference but not explicitly stated, a trend that seems to color the fandom's perception of another issue in the series, mainly the statistical extrapolations and implications about the geth and quarians which seemed to escape many players' notice around ME3, though some of that may be just from players that only bought the third game due to the marketing campaign. This is a failing on Bioware's part, not the players'.
Did you miss something? Not really, at least not much that was in ME1, and too much depended on complicated inferences that ALSO required sequels; as a standalone game, you did indeed point out plotholes that were filled later.
If you want the plot of any ME game torn to shreds and every plothole identified, you can find Smudboy on Youtube for his series of videos on the subject ("plot analysis").
Nazara needed willing indoctrinated subjects that it can exert control over without having to make its own will known. Saren had a strong will and knew he understood what he was going through, and taking on additional augmentations along the way the Reaper had access to meant that no matter how strong his willpower was, it didn't matter in the end as the reaper had control of his body and mind in the end.
These Geth that follow Nazara it later turns out, they willingly served Nazara on its quest because they believed it was a machine god, however to Nazara and the rest of the Reapers it felt disgusted by the Geth and their fawning over them.
The important thing here is that the Geth were not indoctrinated, they chose to serve the Reaper when their runtime processes agreed to leave the rest of the Geth consensus behind to join the conflict. So with an already indoctrinated Saren acting as Nazara's emissary regardless of his own intentions, the Geth took those orders from Saren because they believed the Reaper would take note of this alliance and see them as worthy.
To Nazara all it wanted was to open the mass effect relay on the Citadel and bring its brothers and sisters through and everything else was a means to an end, including the Geth which would be destroyed the moment that connection had been made.