I understand that most people were expecting the 'Dark Energy' plot in ME3 due to the hints in the second game, but I really didn't know ANYTHING about the whole Dark Energy thing until I started reading people talking about it. Maybe it's cause I really didn't like Tali, maybe because it was too subtle for me, whatever the reason, I honestly never had the whole 'Dark Energy killing the universe' going through my mind. My assumption when playing Mass Effect 2 was that the Reapers were focusing on humans because it was a human who screwed the pooch for their plans. The Human Reaper at the end of the game just meant to me that Reapers used other species to create Reapers, and initially I did not realise that it was only the core and that it would eventually be covered in squid armour once built.
I knew about the Dark Energy thing (I love Tali [no not like that, she's just a fun character with a good development arc]), but I never really though it was a big part of the Reapers' motivation. If this was an ongoing natural thing they were trying to stop, it seems like it would have been more widespread and normal astronomical study would consider it normal, instead of being the big mystery to investigate. I figured it might be a trick by the Reapers or the Geth or some other faction that you'd have to deal with, or maybe something you could harness as a weapon against them, or maybe just a weird thing that doesn't enter the plot except as an explanation for Tali's presence there.
Based on what Sovereign said in the first game, I figured that maybe the Reapers were studying the younger races' development. Or maybe they lacked that creative drive of the young races, being ancient and mechanical and immortal, and harvested whatever new technologies were developed by the little mayflies every 50,000 years while being careful not to let them get powerful enough to pose a serious threat. Or maybe they had some motivation incmprehensible to us mere mortals, being the timeless eldrich monstrosities they were. The only things that were certain were that there was nothing above them, they acted only on their own inscruitable interests, and they were confident in their own power to the point where failure was inconceivable to Soverein. But Shepard managed to kill one of them, through trickery and playing on his hubris and impressive leadership and a hell of a lot of luck, so Humanity (and Shepard in particular) got their attention.
The second game gave their reason, or at least one of their reasons: they use the galaxy and the young races to reproduce. While wiping out anyone who might become a threat, they ascend the dominant race, or the best of them in the case of a balance like in the current cycle, to Reaperhood. They're effectively the ultimate social darwinists, giving whoever competes best in the galactic arena immortality and a place in whatever society they have out beyond the rim and exterminating everyone else. Humanity got picked this time around because Shepard proved their potency when he killed Sovereign, and because of all the nice special qualities that took humanity from the first rockets to full Council race status in a couple centuries. If you bring alien squadmates to the final battle in ME2 Harbinger will even tell you why each other race wasn't chosen: the Krogans would have been great if they won their war but the genophage makes them worthless, the Quarians are brilliant but their physical frailty disqualifies them, the Asari's long life and superpowers stagnate their development and their reproduction makes them dependant on other races to produce anything but inbred idiots, etc. Some people thought it was silly (probably because all you see of this process is a giant metal skeleton fetus), but I thought the end of ME2 explained the Reapers pretty well in an incomplete way that would be built on by the third game when you face more of them and have more sources of information; they had a believable motivation that could be added to but didn't need more, and it easily allowed for the same superiority and conceit that Sovereign displayed in the first game.
Then of course the ending of ME3 threw everything away and made them the mindless pawns of a retarded glowing infant, but I choose to believe that didn't happen since it contradicts all of the lore and the major themes of the story until then.
I also didn't mind the direction they took with ME2 being more filler gap before ME3 as it had served a few purposes for the players. It gave us new and more interesting squad members (Kaiden, Ashley and Tali in my opinion were somewhat dull in the first game) such as Jack, Mordin, my main man Grunt, Legion, and to a certain extent Miranda. I liked the begining as it was the perfect way to make the enemy of the game look threatening. I justified the Reapers using the Collectors to attack human colonies as they (the Reapers) wanted humans out of the way due to a human halting their plans. I also enjoyed the more streamlined levels and areas were, as in ME1 I would find myself getting lost or bored in areas such as the Citadel and Feros (if Feros is where you fight the Thorian).
I definitely agree on all of this. ME2 is a prefect example of a second act. The basic stage was set and the big players had been introduced by ME1, but we didn't know much about them. The first big conflict was over and there was hope, but the threat was far from gone. ME2 did what the second in a trilogy should: it progressed but did not resolve the main plot, it grew the hero from where he was in the first act (needing the combined forces of the entire Council and then some plus an overconfident enemy and a lot of luck just to take one target) to where he needed to be for the third act (capable of fighting a desparate, not quite hopeless war on a galactic scale), and it did that well. It introduced all the real players who hadnt been in the beginning, and gave you much more information and development for those who didn't have much of a chance the first time around (the Geth, the Rachni, the Quarians, the Krogan, Aria, The Illusive Man, all your new squadmates, all your old squadmates except for the boring human ones, etc.).
Maybe most importantly, it introduced a real villain to rally against. Sovereign was powerful, but so full of himself that he went into solo combat in a borrowed corpse against someone who killed every opponent he faced on a scale smaller than a dropship. He had no subtlety, no careful plans, nothing in his toolbox but a really big hammer and he got killed in the first act because of it. Harbinger, on the other hand, seems silly on the surface but gets dangerously genre savvy when you look closer. His first action when he takes command is not to brag, or make a show of force, or even to move forward with the invasion. His first action is to find the man who killed his predecessor, and apply enough power to qualify as overkill on any other target to the ship he's on. Then (if you read the comics, or just look closely enough at Liara's story between the first and second games) he does not just count you as dead after your ship was disintegrated around you. He dedicates all the resources at his immediate disposal to confirming the kill, and it's only the combined efforts of Liara, Aria, and Cerberus that manage to recover your body before the Collectors do. And when you come back and do start fighting him, he's learned from the previous villain's mistake: despite the memes he never actually takes direct control and fights you himself, because that's what made Sovereign vulnerable for the moment it took to destroy him. Instead, he always goes through the intermediary of the Collecter General and lies to you at every turn. Then when you complete the main plot of ME2 and somehow make it through the suicide mission? You accomplished next to nothing. You exterminated a handful of second-rate minions, and prevented them from making a human reaper until they could fully subjugate humanity, but all his important plans are intact. And you've alienated the Council, used a lot of resources, and probably gotten several of your friends (the best in the galaxy for fighting Reapers) killed in the process. When Arrival comes you manage to set him back... by a few months, at the expense of immobilizing yourself for those same months, driving every civilized race furthr against you, and all but declraring a personal war on the Batarians. Harbinger might not have as much direct force to bring to bear as the dragon in the first act, but he's smart and he's patient and he does not underestimate you, making him a huge threat and a sort of evil opposite to Shepard in the war; as you scramble to unite the races and organize things against the Reaper invasion, he would match your every move arranging his already overwhelming forces to even more lethal effect and braking apart your fragile alliances.
Until of course the third game appears, Harbinger reads the script, and opts out of the whole mess.
Mass Effect 3 focusing more on Earth made sense to me due to my inability to understand that Tali's mission hinted at a different story for the Reapers, and I reasoned their focusing on Earth was due to a human ruining their plans twice, so this was payback for being awesome at stopping ancient synthetic/organic space ships. I understood that some people were angry because they wanted to explore other planets, and Earth seemed dull to them, but I felt that really drove home the fact that just because we killed 1 Reaper, a bunch of mutated Protheans, and a baby Reaper, Humanity and the rest of the space races were hopelessly outmatched.
I believe every major race's capital/homeworld recieved similar treatment as a major invasion and harvesting point, but it does make sense for Earth to get special attention; if Shepard, TIM, Joker, Anderson, and all those other big time players came from humanity, Earth is a source of many potential threats, and if they're still the best choice for this cycle's new baby Reaper you need your biggest harvesting operation where the human population is biggest. And personally I was kind of hoping for more missions on the surface, sabotaging reaper operations or extricating VIPs with the Normandy's stealth drive.
What doesn't really make sense is using Earth for the ending, or trying to rally the galaxy to take back your planet specifically instead of generally beating back Reaper forces, but nothing in the ending and little in the core plot makes sense.
While I still love the series, I can see how Bioware kinda screwed the pooch when it came to Mass Effect 3 as they had built up so much hype and expanded on the universe with novels and comics. But I just got really annoyed when people started demanding a new ending and picking apart thngs, especially when some people started pointing fingers at ME2 even though weeks prior to ME3 they liked the game.
I still love Bioware. You can see the old brilliance and talent they made so many classics with throughout ME3, and they actually lived up to the hype for the most part... outside of that 10% containing the ending and the Crucible. And then you can see EA's bloody handprints all over that part, after the lead writer of the first two games was replaced. So as much as I hate to say it and as much fun as I've had, I don't think I'll ever be buying another Bioware game.