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Giant Eagles in a fantasy setting are less likely to break suspension of disbelief than the question of why they weren't used to get to Mordor in the first place, (if no obvious answer is given in the narrative). And yes, Giant Eagles is an issue of suspension of disbelief, albeit not much of one in a fantasy setting, but so is answering the question of why they weren't used.
If you're combining plot holes and suspension of disbelief, which makes sense because plot holes can strain SoD, then I understand. However, the original conversation separated the two, which is why I said what I did.
Bioware has already done that- "Leliana dead? I don't think so, players." "You killed the Rachni queen? We found another one." "Destroyed the Collector base? It didn't even slow Cerberus down." "Your Revan was a woman or wasn't interested in bratty Bastila? Too bad, our Revan impregnated her and started a Shan dynasty."
To be fair, the Revan one is more excusable because they are working within someone else's IP.
The better question is: How did Saren/Sovereign even know about the Conduit?
Follow up: Why would they go to all that trouble, exposing themselves and warning the galaxy of the Reaper threat if there are a much easier ways for a Spectre to walk into the Council chambers (you know, like Shepard does all the time)?
Another question: Why draw attention to the Thorian with the attempt to destroy it? No one would have known about it without the Geth attack.
Yet another: Why would Sovereign go to Eden Prime itself, if Geth ships could do the job just as well?
Last one: Why clone Krogans? Whatever are they good for?
Yes, how they knew about the Conduit is a great question. As for there being easier ways to get to the console, that was the mistake of using the Council chambers. As much as I like the Relay Monument being the Conduit, up until that point I thought the Conduit was going to take us to the hidden parts of the Citadel.
The Thorian is a simple villain mistake. He's attempting to cover his tracks but it backfires. He probably didn't know the colonists would protect the Thorian.
On Eden Prime, why not? Sovereign wants to make sure Saren gets to the beacon and Saren is riding around on Sovereign anyway.
As for the Krogan, they are perfect shock troops. They will be useful for the overall extermination.
Err 'The shepard' epilogue is not taking the three games and saying 'it is all a story.' It was an older generation telling the younger generation about a great war that everyone living today owes their freedom to the people who fought it. Much like how people talk to children about WWII and why it is important to remember those who fought in the war. It was a clip showing that the future generations that "The Shepard" saved remember. They remember the war and what was done to save them It was not saying its was all a story. The fact that you got that from the clip explains why you think ME2 they suddenly out of left field went on the Messiah kick.
You don't seem to be judging scenes in the context of the series but judging them in isolation. ME1 clearly shows the messiah story was INTENDED, because they added aspect that fit the messiah archetype before ME2 and they continued them through all three games. ME2 and ME3 provides the context to show ME1 intended the Messiah story. If you just took ME1 alone in isolation there isn't enough proof to definitively say it is a Messiah story but why would you do that? Why view ME1 in isolation when it is part of an interconnected series?
When I say it was a story, I don't mean that it didn't happen necessarily. I mean you're not playing the events as they happen. The entire 3 game series is that old man (or woman with refuse) telling that child the story of "the Shepard".
You can always look at earlier works in isolation, especially if things weren't planned out as a whole, because later work can change the meaning of something that happened earlier. An easy example is Star Wars. When A New Hope came out, Darth Vader was not Anakin Skywalker. Obi-Wan told Luke the plain truth. The idea of Vader being Luke's father came later, which changed what Obi-Wan said, requiring the "point of view" conversation in Return of the Jedi. Further, things that happen in the Prequels make you look at things in the Originals differently. So while you can't look at ME2 without the context of ME1, you can look at ME1 alone because it came first. I can easily argue that you only see the things in ME1 as the Messiah archetype because it's so blatant from ME2 onward.