One thing I hate about discussing the trilogy in general

This makes no sense at all... Saren wanting to increase the amount of resistance he is facing during an attack?  A covert attack, prior to exposing himself via the Eden Prime attack, would have gotten him closer to the master control unit (council chambers) with fewer casualties to his troops than the frontal assault (just using a "conduit" to drop him onto the public plaza in front of the Tower).  A few people suddenly pulling out weapons during a council meeting would have ended the Council immediately.  How many people are there shown in the game standing around the Council chambers during Shepard's inaugeration? Maybe 15.  There were even less when they were first accusing Saren.  The squad aludes to there likely being some snipers out of sight, but still not really enough that Saren, with a few commandos, couldn't easily take them out, especially because they would have been totally surprised... having total trust in Saren (their best Spectre agent).

Saren could have then used the Master Control Unit and shut down any external defenses before C-Sec would even be aware anything was happening.  Asari commandos could be stationed covertly throughout the Presidium to "surprise" C-Sec officers in various locations simultaneously, thinning their numbers before, again, they're even aware of what is happening.  Saren would also have a number of Krogan at his disposal (again, if he had not tipped his hand at Eden Prime), who could have been stationed covertly in various locations throughout the wards (like in the C-Sec area) and probably been able to easily overrun the officers there by first catching them by total surprise.  He could also have a bunch of geth hidden on a docked ship (of normal design) - since it would seem totally normal for a Spectre to arrive at the Citadel on a normal ship.  The amount of fire power he could bring to to bear on the Citadel via a covert attack would be actually far greater than the amount of troops he was likely able to bring through that "mini" Conduit and he could get them onto more varied locations on the Citadel without detection than having them all drop into only one location.  In a more covert attack, he would suffer fewer casualties and inflict more "surprise" casualties on C-Sec before they even realized what was happening.

Once Saren has control of the Citadel via using the Master Control Unit, the Citadel's defenses are down and Sovereign could appear through the regular relay and just drive on in.  The Alliance fleet wouldn't be alerted to anything, so would not be a factor.  Also, by having gained Master control of the Citadel quietly, Saren would have air control over all the Citadel air space and could direct ships into docks normally and ambush them there or use an excuse to put them into some sort of holding pattern.  (This is a bonehead move by Cerberus in ME3.  They should have answered Joker in a normal fashion, bring him into dock and surprise Shepard as he walked off the ship.)

Back to ME1 - Again, Sovereign must have known of that Master Control Unit since the Reapers built the thing to start with.  They already know that the keepers aren't doing what they're told.  That's self-evident since they aren't trying to open the relay; and Saren could walk through the Citadel any day of the week and just see that the keepers aren't responding to the signal.  It doesn't really matter that he find out it was the Protheans who did it, which is the only additional information Vigil can given Saren beyond what Sovereign and Saren already knows or could have easily seen for himself just by quietly observing on the Citadel. 

It might have been better plot-wise, if Bioware had written it such that the Protheans were the ones to have installed that Master Control Unit and that Sovereign was unaware of it's existence... but they didn't.  Alternatively, they could have set it up such that the Protheans did tamper with the Master Control Unit, making it necessary for Saren to have that data file to get things working again... but they didn't. 

Additionally, if ME1 had done a better job of setting up for the rest of the Trilogy more clearly, then that Master Control Unit AI (installed by the Protheans) could have been revealed as the Catalyst... just needing the Crucible to be installed to be activated.  It could have then been easily described as a virus activated within the Citadel systems the moment the Crucible docks and the manner in which it infects and affects the Reapers left in place as the decision of the player (basically, repeating the pattern set up by the Heretic Geth decision in ME2).  Instead, to it's own fault, ME3 diverts the plot farther afield by instead revealing the Catalyst to be some sort of dominant Reaper entity AI created by the first race to be harvested... suddenly introducing a whole new species near the end of the Trilogy in the form of a DLC.

The bombs Saren used on Eden Prime are clearly described as being "nukes" (by Maeko Matsuo on Feros if Shepard indicates that the reason he/she became a Spectre is because he saved Eden Prime.  She responds with "You're the one who disarmed the nukes...").  So, Saren has the means.  Saren is too rushed because, obviously, you're wrong, the Trench Run is minutes long, not hours and Shepard is hot on his tale.

Avina #2 can tell him, if the player inquires with her; but Shepard will bee-line for the Citadel Tower even without triggering the conversation with Avina.  As I said, one problem in this part is that the same Avina #2, earlier in the game, will clearly tell Shepard that Citadel Control is in the Citadel Tower; but the Emily Wong quest sends Shepard to Citadel Control in the wards up the stairs from C-Sec.

The only reason Saren has to ambush the Citadel using the Conduit rather than a more efficient covert attack is because he foolishly blew his "cover" as a Spectre (i.e. destroyed the unlimited accessibility he had to virtually every known area of the Citadel) by attacking Eden Prime for information he really didn't need and that, ultimately, was no real assistance to him.  That's precisely why, in my opinion, the ME1 plot undermines itself.

I agree.  The discrepancies, in several ways, are suggestive of a significant change of course partway through the writing.

Shepard knows... and he/she does not correct Matsuo about it being a nuke.  Why would you assume the line was originally meant to refer to Virmire... Shepard sets the nuke on Virmire, he/she does not disable or disarm it.

There are also a few problems with just assuming that the Trench Run took hours for Shepard to complete.  As as been said, clearly Shepard arrives on Ilos only a short time after Saren.  All Saren has time to do there is quickly close the door.  As both Han and I have indicated, Vigil clearly indicates that, at the point where Shepard starts the Trench Run, Saren has not yet even reached the Conduit.  As Han has said, the Conduit is still active from when Saren used it, so that Shepard can just drive into it with the Mako.

The reality is that the story plot is a mess... which is what I've been saying all along.  ME1 ultimately has a lot of its own flaws and doesn't do what a proper first installment of a Trilogy should do... that is, provide a solid foundation on which the finale is ultimately constructed.  ME1 is to blame for the ultimate mess that is ME3 AS MUCH AS the flaws created anew in ME3 are to blame.  Add in the fact that ME2 does nothing to advance the main plot (which is what a 2nd installment of a Trilogy should do) and it is obvious that I'm assessing the blame 1/3 to each installment.

When Saren sees the Normandy, he was on foot. Did he walk all the way to the conduit? Or did he call a taxi? If he did walk, Shepard might have caught up to him before he reached the conduit. Don't know.

So a man with a geth army at his back, and a few krogan clones and asari commandos runs from a guy with crew of just six, while counting on doors and small squads said pursuer has already been blowing through like tissue paper this entire time to stop him? Here's an idea, get those four Colossi by the trench run, and back them up with iike ten more and also about 100 other combat platforms of all sizes and shapes, with a couple of dropships for air support. Then have some asari and krogan flank them when they rush in, box them into a kill zone and turn them into swiss cheese vaporized specs of dust while chomping on a space cigar. Then activate the Conduit and stroll through like a boss. What's that? Then you wouldn't have a game? Welp, that's what I've been saying about the Conduit from the start! Some things you can poke, some you leave alone because video game.

Because you don't talk about any variety of plot discrepancies. You just go back to the Conduit every time. And your past couple of replies have read like a refusal to engage the argument at hand (I had to ask you three times why Saren's running) in favor of simply restating "the Conduit sucks". You've broken off the argument to restate your conclusion despite the fact that we haven't finished debating it yet.

Well, I think a wiser course of action would be to agree to disagree. It seems we've taken this discussion as far as it'll go.

Fine by me.  I've tried to answer your questions and you're not happy with those answers.  Agree to disagree works for me.

I know this is cheating but I'm reading the comics by Mac Walters and sometimes other writers. The ones written by John Jackson Miller are actually pretty decent.

In Foundation 3 we get the events prior to the opening of ME1 when Ashley loses the 212 on Eden Prime. At one point she says it's been over a day since Saren's attack and this is before ME1's opening. Weren't it all really urgent while Shepard received the transmission from Eden Prime? Did that transmission really come one day after the attacks started?

Thoughts?

A few krogan and asari take on C-Sec HQ (while also providing the general chaos and drawing away forces I mentioned)? You must be joking. Winning ground is precisely what needs to happen since they're not raiding a bake shop here. The fact that they don't intend to hold it afterwards is irrelevant. Saren needs enough troops to fight through C-Sec and back out again, up to the tower. Even if it's a one way trip for all involved, there's multiple stops and loop. Also when you already a geth army why the hell would you not use it?

Saren made one mistake. Just one. He used violence at Eden Prime instead of deception and he left witnesses. He needed the beacon (because at that point no one knew what it did or what the Conduit was) he should've showed up with Benezia, a spectre and a matriarch here to take the beacon, wham bam thank you goodbye. And that's it. Instead he decided to torch the place. A stupid mistake, but even so it can be justified by his character. He's arrogant, hates humans and likes to cause carnage. He actually would've gotten away with it too if not for the most unlikely chain of coincidences (and also these pesky kids): a random quarian (a rarity round these parts) recovering geth memory which never happens, who travels to the Citadel and evades assassins by way of Shepard literally wandering down a random alley. Without these events happening exactly as they did, our heroes would've had precisely dick to a) strip Saren of his Spectre Status, promote Shepard to the Spectres and thus c) gather the band and gain command of the ship that would prove his downfall.

If Tali wasn't available for the audio file, there would be another way to find evidence against Saren. Udina mentions they lost comms with Feros and there were reports of geth in the area. Shepard heads there. The same happens as in the game, but instead of killing Shiala or leaving her on the colony, take her back to the council to tell the council the same thing she told Shepard.