Nice points you got there. Juicy. First thing I'd like to point out is that although I am familiar with both Pirates of the Caribbean and MCU I'd like to keep our discussion within the boundaries of Mass Effect because if I wasn't familiar with Pirates of the Caribbean or MCU then I would have trouble understanding you.
Back into the main stuff.
You bring an interesting point that ME2 is written with the sequel in mind unlike ME1 however I beg to differ (yet another sidetrack from our discussion). You are right that ME1 is a self-contained story. It is consistent, it flows naturally, it has a great conclusion. But it's not because it was unsure if the sequel would follow. I may be wrong but the gaming industry is different with their plans about future installments. Sequels don't depend on the success of the predecessor. There are several examples of the games that produce sequels regardless of the quality or reception of their product (Assassin's Creed or any other example of yearly relase of the new title). And there are examples of the opposite - when after the successful game the sequel doesn't come (lack of Half-Life 3 even became a meme). And ME1 was totally created with the sequel in mind. Mainly because subplots like the Cypher, Genophage and Morning War don't really have any resolution, they were only established into the series. And the way Shepard finishes his line "The Reapers are still out there and I'm going to find some way to stop them" which sets up the overarching plot which will be in the sequel.
However when ME2 comes out it actually doesn't feel like a sequel we deserve (I won't go into the details for now).
I actually like your idea that ME2 and ME3 are a two-parter. It is a great approach, there are several films that did that right. But this doesn't apply to ME2 and 3. First thing I'd like to clarify about ME2 is that it is a self-contained story like ME1. It has a beginning (Collectors attack human colonies for some reason and only Cerberus wants to do anything about it), it has a middle (Collector Ship mission that is TIM's trap), and it has an end (Suicide Mission and breaking up with TIM)
Back to my original point:
It is a separate story about the Collectors. A major side quest. It doesn't advance the Reaper plot in any way, just gives a bit of flavour on their Harvest. The overarching plot portion of ME2 is...5 % at best if you count Arrival with the rest 95% coming from ME3 (and of course it failed). We don't learn anything about the Reapers, we just have a reason to fear the Harvest. And ME3 tries to do ME2's job and establish its own plot...So we have a Crucible revelation (a way to stop them) then we have some info about the Lazarus Project thrown in the last act (a contemplation of whether Shepard is still Shepard)...then we have the Leviathan DLC that tries to explain the whole Catalyst nonsense... and that's basically it. All of this should've been in ME2 for it to work as a groundwork for ME3. Instead the whole Collector-Cerberus stuff was distracting us from the main plot when this time could be put to good use. I don't mind the Collectors being in the game. I just wish it tied better into an overarching plot so it would be meaningful in stopping the Reapers or learning about how to stop them.
About ME2 characters and their importance. You described nicely the ones who are replaced due to their importance to the plot. But don't you think that if you can easily replace them then this importance fades away? The only good example is Thane (and Kirrahe): He doesn't really do much in ME3 and Kirrahe just had one badass shot on Sur'Kesh but they are crucial in saving the salarian councilor. If you don't have them then he(she) dies and there's nothing you can do to stop it (for some reasons).
Other characters are only important in side missions (Jacob is not important at all though) and some can be replaced by random new filler characters.
Even Wrex (the guy who you can kill off in ME1) is more valuable than any of ME2 characters because his presense is crucial to the resolution of Genophage arc. If he is there then it makes sense to cure the krogan but if Wreav is the clan leader then it doesn't seem like a good idea. It's funny you mention Grunt because he was absolutely pointless in ME2 (he isn't useful in any role in Suicide Mission) and he is absolutely pointless in ME3 (he gets replaced by a random less badass krogan without the catch-phrase) but the presense of Rachni is a mockery to ME1 players who chose to destroy the last queen.
And the last part.
You say that organics are helped all along the way but wasn't it true to Geth as well? The Catalyst has one task: to preserve organic life from being destroyed by synthetics. What does it end up doing? Helps Geth destroy organics. First in ME1 as Sovereign and then in ME3 when the Geth were desperate. If your task is to preserve organic life and you see that this very organic life actually has good chances against synthetics why would you interfere and help the opposing party? Here's an example: You meet 2 kids. Let's name them Gary and Kevin. Gary is a bully. You want help Kevin. He doesn't ask for your help though and he actually manages to avoid Gary. Next time you meet them, Kevin kicked Gary in the nuts and he is crying so you decide to help him instead. You propose him assistance to bully Sam further if he acknowledges your authority and he agrees. Does it make sense to you? To me it doesn't. The point being, if organics are helped by Reapers manage to resolve the conflict with synthetics who are helped by Reapers then shouldn't it make it even?
Furthermore, after the Crucible is attached, the star child says that it altered his variables and it means his solution won't work anymore. Yet if Shepard refuses to play his games he gets all angry and says "the cycle continues". What? Suddenly his solution works? Why is he able to create only 3 terrible solutions? Why can't we persuade Catalyst of its faulty logic? Why is the Catalyst so inconsistent? I'd like to know your input on this and I don't want to encounter any head-canon stretches, just what was actually presented in the main game.
You don't really need to understand the PotC universe to understand my point. Simply know that Disney created the original movie as a one shot stand alone movie. How ever it became so popular they green lit 2 squeals to the original movie. Adding new things not hinted at in the first movie to allow it to be stretched over 2 movie turning it into a trilogy. Which echos how ME trilogy came about. ME 1 is created as a stand alone game. It's popularity allowed them to create squeals which they then had to rework stuff to allow it to be able to expand into a trilogy.
The game industry is a lot like the movie industry they don't take new ideas very enthusiastically. It is why you seem to be seeing the same movies made over and over again and some of the biggest AAA titles are the same games remade or a squeal to an older one. Your mention of Assassin's Creed fits that completely. As they have basically been reskining the same game with new gimmicks for years. New game can either be a complete bomb or simply are not popular enough to warrant a squeal. Bioware went the route a few games and a lot more movies should go down. Their first game in the series was a complete story. If it bombed or was not popular enough for EA to green light a sequel it still told a whole story. It how ever left enough open that if a sequel was allowed they could pick up the story and continue on. This is why there are some pacing issues with ME 2 and why it seems to some people like you as completely negating everything that happened in ME 1.
The Collector activity is a direct effect of you killing Sovereign in ME 1. If Sovereign wasn't kill the Collectors wouldn't need to start harvesting humans as the Reapers already were. Up to that point in the game world the Collectors have been so mysterious as to be considered on par with big foot on them not existing. They are only spurred into action by Harbinger to become more direct AFTER the events of ME 1 and Sovereign's destruction. Hence why the first thing they do is attack the Normandy to kill Shepard. Before they start attempting to harvest humans to create a new Reaper to replace Sovereign. Showing even if they are locked in Darkspace the Reapers can still spread their influence on the galaxy. The destruction of the Collector base is what prompts Harbinger to tell the rest of the Reapers to saddle up and head towards the Galaxy because they have some advanced organic and synthetic life to harvest. ME 3 isn't a stand alone game because everything about it depends on your knowledge of previous games.
No their importance doesn't fade because them continuing to exist depends on your choices in the game. Choices are a core part of this game. Even if someone else shows up in their place it is my choice in previous games that dictate if they show up or not. This allows players to be space jesus or space devil and not be told they are playing the game wrong. Jacob still fits into the over all story line showing that there are people simply wanting to survive the Reaper invasion. Jacob could join the fight but he is far more interested in starting a family. Jacob was always set up to be the every day man. He joined Cerberus not because he agrees with them but because he saw them as the only group actually doing what is needed to help people. TIM even out right states in ME 2 how Jacob has always been willing to vocalize his dislike of certain actions TIM has taken. Those that he is aware of anyways. Jacob might not play a role in the beat the Reaper part but his role in showing what people are fighting for is just as important. Grunt is the catalyst that bring you to Tuchunka were players learn more about the Krogan and their daily lives. As well as showing the effect of your choice on Virmire. Grunt in ME 3 plays a really large role in the Rachni problem. Which doesn't actually spit in the face of anyone who choose to kill the queen. As the replacement is a synthetic Reaper creation. If you choose to do anything but destroy the fake queen your an idiot. If you saved the queen you are left with two choices. Save the queen again and risk Grunt and company or leave the queen and ensure Grunt and company survive.
You kind of land off target with the Geth. Sovergein uses the Geth as a portable army to open the Relay and allow them to jump right though. The funny thing is that action doesn't actually prevent the Reapers from then turning on the Geth and harvesting them to. Much in the same way it wouldn't have stopped them from harvesting Saren. Harbinger actually has some quotes about the Quarians
http://masseffect.wi...)/Battle_Quotes
“Quarian; considered due to cybernetic augmentation, weakened immune system too debilitating.”
Lets also not forget the final show down that results in the complete death of the Quarians only happens AFTER the Geth are freed from Reaper control. The Reapers could easily have wiped them out before Shepard shows up but they choose not to.
And with the Curible you again miss the context of the words. The Crucible opened new possibilities the solution was in danger of failing not because of the Crucible. But because the factors in the galaxy were changing. Refuse ending shows the next cycle finding Liara's time box things allowing the next cycle to be more prepared. That is the reason the Catalyst mentioned it's set up is failing. Each cycle was able to pass more information to the next.