I'd question how much the Two Towers was essential to that saga. Sure you beat Saruman but that was a side show. I guess the ring got physically closer to Mordor. Empire didn't actually "do" anything about the Rebel/Empire arc other than finding out about Daddy issues. Oddly both movies really didn't "do" anything but they were the best movies of the lot. The second act is always tough because it is connective tissue more than exposition or climax like parts 1 and 3.
Still in 2 you learn about the fate of the Protheans which is sort of a big mystery. You learn that Reapers use the races against themselves, which forshadows a lot of what happens in 3. You also obviously get a much closer view of Cerberus which does matter because unlike Saruman's horde Cerberus does matter a lot in the third part. You stop construction of another Reaper in a terribly bad boss battle and also save a whole lot of people. I will say I wish the Arrival DLC was integrated into the base game. It works perfectly as a bridging content but it would have added more umpf to the impact of the base game. To some extent if anything too big happened in 2 it would have undermined the effect of one. One was supposed to have thrown a major wrench into the Reapers plans but if they had shown up in 2 in a big way then the "what was the point" question could be asked.
Two Towers: Party splits, Boromir dies (in movies these were pushed up into the first one). Gandalf comes back from the dead. Saruman was a side villain yes, but he was helping the main villain, would have been another enemy to fight, and was trying to wipe out the help that Gondor ultimately needed. Frodo and Sam meet up with Gollum, who poisons Frodo's mind against Sam. setting the stage for the end, and Frodo is "killed".
Empire Strikes Back: Everything that happens on Dagobah. Han and Leia find and accept their romantic feelings for each other. (Though I suppose that's more character development than main plot.) The scene where Vader is in his pod with his helmet off is important in expanding on his character, which actually is important to the main plot.The duel between Luke and Vader, which included the temptation as well as the reveal that Vader is Luke's father, and ends with Luke accepting death over siding with Vader, though he luckily survives. Han goes to Jabba, which sets the stage for the 3rd movie's opening act. Also, the movie reminded us that the Empire was a real threat that wasn't defeated just because the Rebels destroyed their super-weapon.
Mass Effect 2: Nothing.
Shepard's death is meaningless. The Normandy's destruction and remake are meaningless. Collectors = Protheans; meaningless. Destroy or preserve base: meaningless. You get EDI,which could have been done anywhere and in any way, including as an addition between ME2 and ME3 and while she was plot critical in ME3, that had to do with fighting Cerberus, not stopping the Reapers. Her gaining personality and relationship with Joker could have been a great argument against the Catalyst's premise, but they didn't do that. Malon's data and the Geth Virus are optional side missions and are still not plot critical to ME3 since they just affect War Assets.
Vigil told us about the fate of the Protheans. They were annihilated. There was no mystery. Collectors = Protheans was just supposed to be sci-fi horror twist. Because we met Vigil, it didn't work. Had we never been told what happened to the Protheans; had they just disappeared, this twist could have worked. Vigil also already told us about Indoctrination so we knew the Reapers "use the races against themselves".
Cerberus was not important. They became the main antagonists of ME3 for no reason. There was no reason for the human Reaper to exist and destroying it didn't lead us closer to beating the Reapers. Arrival was cool but ME3 made it moot because nobody did anything with the extra time and they retconned what happens when relays get destroyed, which is why they changed the cutscene in the Extended Cut.
The Catalyst made us ask "what was the point of Mass Effect" because they had a consciousness on the Citadel that had no reason to not be able to control it and let the Reapers through the Relay. Nothing "big" had to happen in ME2, it just had to tie into the goal of "stop the Reapers".
People seem unnaturally worked up about the RGB quality of the ending. DAO was an RGB ending, just camouflaged better - and really for each character it boils down to Dark Ritual or not so it is RG. Nothing you have chosen to that point matters. Then again so was ME1 -- there is no scenario where Sovereign doesn't die and the RGB choice is save the council or not and nothing you have chosen to that point matters a whit in what you pick.
Don't get me wrong, the ending was terrible for a lot of other reasons but the basic mechanics just exposed the wiring a bit too much. People lament the change of writers but frankly the dark energy ending I have read about was every bit as grim - reapers are trying to solve dark energy problems foreshadowed on Haestrom - and your choice is save lives now and doom the future by defeating reapers or let them win and doom trillions now to save the future. I don't think there was ever a sunny beach ending for this thing.
The problem with the comparison is that Dragon Age Origins was a self contained story. Most of the choices had no plot impact but you got to feel like you influenced the future of Ferelden through the well written epilogues. Mass Effect 3, on the other hand, was a third chapter of a trilogy. In addition to being built on two past games, we were promised wildly different endings by the developers. Was such a claim made of Dragon Age: Origins or Mass Effect?
There is also a significant emotional and tonal difference between someone making the Ultimate Sacrifice and both Warden's returning alive. The same is true for the 3 possible endings to Mass Effect. (Council lives, New Council with human chairman, and new Human Council with human chairman.) There really was no such difference in the three endings initially. The narration of the Extended Cut helped a bit, but they were still all disappointing.
Well the Dark Energy plot was just a shell, so I'm sure they would have done more with it. The idea would be that saving lives now does not automatically doom the future. The races would try and find their own solution. Maybe they will fail, but maybe not.
I was particularly annoyed by organics-synthetics because at the time I thought it infantile. Like a non-issue that they decided to implement as the crux of the series. 'Things will always fall in a gravitational field' sort of stuff.
It was a B-plot they decided to make the main theme for no reason.