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It's not rocket science.
1. I agree it's before the Reaper invasion
2. Shep gave a goodbye message to the ARKCON crew, She knew and not doubt Hackett also.
3. Earth was establishing colonies all over the galactic map. It's unsurprising they found many who wanted to leave for a "better world".
4. "Big secret"? The Alliance Initiative had no obligation to tell them the exact location or could have simply lied to them or did a superb Bio marketing trick by telling prospective colonists that the Alliance found a new location away far away from the Reaper Threat.
5. Promethean tech was reverse engineered. For one, the Alliance had an actual stasis pod from Javik .
No, there will be no retcon, I assure you. It would be too messy. Besides, Bio has no obligation to explain the tech for the trans-galactic voyage and the ARK's engines.
"It's not rocket science." - Traveling 2.5 million light years with technology inferior to Reaper tech.
Of course, they could have found another ancient technology from a species outside the milky way to cover this, but didn't use it to fight the reapers, or mention it at all.
"Shep gave a goodbye message to the ARKCON crew, She knew and not doubt Hackett also." - Yet in all conversations Hackett and Shepard had during the Reaper war they didn't bother to mention their species escape plan, or even the possibility of the Reapers finding out, or any problem in logistics anyone involved could've faced it. Or even when the asari councilor says "plans must be put in motion, continuity of civilization has to be considered...", Shepard didn't mention it at all, to anyone, at any point in the war this huge deal for the survival of their species, in another place, far away from there.
"t's unsurprising they found many who wanted to leave for a "better world"." - "The Alliance Initiative had no obligation to tell them the exact location or could have simply lied to them or did a superb Bio marketing trick by telling prospective colonists that the Alliance found a new location away far away from the Reaper Threat." - So let's all travel to a place we don't know where, away from everyone we know, in a ultra huge citadel-like spaceship because we need to run from a threat the general population has no knowledge of and the government officially denies it exists. But will be exciting, they promised!
Promethean (prothean) tech was reverse engineered. (For one, the Alliance had an actual stasis pod from Javik. - Which they discovered DURING the reaper war.) And the others before it, never turn out to actually help in the war, but were able to turn prothean tech (inferior to reaper tech) into ships that can fly into another galaxy millions of light years away in just a few hundred years.
But what you said is true, Bioware doesn't have to explain anything to anyone, or even make sense, but that is what kills the immersion for me.
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Saren, which never states in the original game he plans to attack the Citadel and there isn't any evidence he plans to do so, but when you are at the endgame, the Council somehow knows he's going to attack them, because you apparently told them.
Illusive Man is affected by the reapers for 30 years, gains a lot of visions and other abilities, like other species languages from them, but was able to resurrect their greatest enemy, and then turn against him/her because he wants to control those ancient machines (which you are forced to disagree it's the best solution), so he goes hunting for the catalyst, but he can't use it without the crucible, so he warns the Reapers to protect the Citadel so the Crucible can never dock there to begin with, to allow him a chance to try.
Trying to reclaim Earth with all your forces even before knowing what the Catalyst is, potentially jeopardizing all the war-effort.
Hackett - "For all intents and purposes, an assault on Cerberus will be the first stage in our attack on Earth"
Kai Lame, appears with a gunship from nowhere in Thessia's temple, but you can't shoot the gunship down (after killing Reapers, thresher maws, gunships, harvesters, spectres) and don't call Cortez for backup, or the Normandy (never stated during the mission you couldn't contact him/them, and how did you returned to the Normandy later?). Shepard doesn't run towards Leng when the temple is collapsing, doesn't charge, doesn't turn cloak on, and no squadmate appears to at least distract him. Or before, in the Citadel, turn the cop car upside down, or stop abruptly so he falls to his death.
Stupidity turns on in the trilogy so we can have these "dramatic and emotional" moments.
"We fight or we die, that's the plan!"
"The Citadel? The fight's here!"
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And if anything, video games (for me) should never insult the intelligence of their customers. Sure as hell want to see how they are going to wrap all this up, if they do.
But that's just me.