I understand where you guys are coming from in saying that ME2 did a u-turn on ME1 or didn't advance it any further. However, let's look at it from a continuity perspective and what ME2 actually puts forward,
1. Sovereign was defeated by a human's endeavor (primarily)
2. What ME2 tells us is that Harbinger (and the other Reapers) are targeting humanity because "they/we got their attention"
3. They're using their proxies (Collectors) to create a Reaper ... that would be more effective against humans? They already have a precedent of using proxies like the Geth.
4. The Collectors are Protheans modified with 'Reaper tech'. Modified and indoctrinated so heavily that they no longer resemble the species they were. A recall to Saren stating that the more control a Reaper has on a subject, the less capable it becomes. Mordin states that the Collectors, so heavily 'synthesized' (my word), are incapable of art and social progression.
5. Cerberus command having the chops to isolate its cells so well that the team investigating the Reaper IFF did not let on details about Shepard's mission to the Collectors. TIM also shows his devious but clever tactics at deceiving the Collectors and ultimately the Reapers. Seems too smart to let himself be indoctrinated.
6. A minor side story about Dark Energy referenced in Tali's mission. That thread could have been taken forward to weaponize entire systems against Reaper fleets.
7. I recently played through ME2 for the 4th time and only now do I fully comprehend Legion's words and his background on the Geth. Especially his lines about 'Geth consensus compared to organic consensus imposed through autocracy or one that agrees upon the lowest-common-denominator (paraphrasing)' and the one where he talks about 'each program or unit offers perspective' coupled with their ability to communicate at the speed of light was fascinating. In addition to this he also talks about the lack of distrust between their own. For a second I was transported to a happy place where something like this may be possible in humanity's future, where billions of people can offer their own perspectives and facilitate co-operation and understanding. Legion also admits to tracking organic society and communications so this entire dialogue could be perceived as a deception ploy to lower Shepard's guards and dazzle him (like it dazzled me). But I find it unlikely. Anyway, the Geth perspective and the parallel infighting in the Quarian fleet was probably the most interesting side story in the entire game and what happens in ME3 is sorely disappointing.
8. The Genophage cure is almost synthesized. Whether you save the data or not doesn't really make a difference in ME3 (I think, I only destroyed it once) but the Salarian guilt (in the lower ranks) about the entire fiasco is made pretty clear.
9. A possibility of Shepard being part machine himself is never actually explored in the 2nd game. The only other time it's brought up is at the end of ME3 when the starchild talks about it. It could have been interesting to explore this further but the 3rd game was so 'emotionally charged' and made so many appeals to the player's 'heart strings' that the culmination of many of the science fictiony aspects of the series' concepts was totally ignored.
To discuss the differences with ME1 and ME3 individually would make for a very large post so let me summarize them in brief,
ME1 introduces the entire story, the background, the species, the technology, the characters, the Reapers, the Prothean extinction, Mass Relays, the Genophage and the history of the Krogan-Turian-Salarian-Rachni quartet, the Geth-Quarian war etc. It's actually quite impressive what they were able to talk about even though most of this information is in the codex and casual references in dialogue etc.
ME2 is the one where the writers somehow made science fiction based on the reality established in ME1 (this paragraph is a little abstract so bear with me). This is no easy task because the science fiction of ME2 isn't based entirely on our own real-world-reality. It's actually brilliant if you think about it. It talks about the points I mentioned above and actually feels different from ME1 because it explores the impact of research on scientific frontiers on society and individual people. This is the time in the series when we actually 'begin' to comprehend the Reapers and their methods with the live example of the Collectors and the 'work' done on the abducted colonists. While the first game was about they mystery of the Reapers and their 'un-knowableness', this games actually parted the curtains of this mystery and acquainted us with 'some' of their activities and intentions. I know stuff like the Lazarus Project and 'essence of a species' is pilloried very badly but there can be no science fiction (or even scientific breakthroughs) without a hint of philosophy and imagination.
ME3 on the other hand, let's look at what it took or discarded from ME2
1. From a narrative standpoint, Harbinger, the Collectors, the Base and the Reaperizing of the humans was entirely ignored and/or retconned
2. Cerberus is a totally different organization with a totally different head of operations (TIM in ME3 vs TIM in ME2). Actively indulges in 'Reaper tech' inspite of the precedent of the Collectors and Saren. Has supposedly unlimited human and financial resources. Regardless, the choice to destroy or save the base has no effect on Cerberus.
3. Dark Energy ... ignored.
4. Rewriting or Destroying the Geth ... ignored. The Quarian's infighting has been resolved and their suicidal attack on the entrenched Geth compels them to go to the Reapers? OK. WTF happened to Legion? Why the obsession on 'being alive'? Weren't they 'alive' enough when Tali's father was conducting weapons tests on regular Geth?
5. My suspension of disbelief is shattered sooner and sooner in every ME3 playthrough. This time it was when Cerberus showed up on the Salarian homeworld to stop the immune Krogan female being given back to the Krogan. Wat? Why does Cerberus have more concern about Krogan than the Turians and Salarians? Similarly, if Cerberus can be taken as representing part of humanity's perspective on inter-galactic relations, why isn't the Alliance more of a war-mongering entity? I can understand the Council dithering because they represent something like a UN body. The entire Genophage arc was soured by the very presence of Cerberus.
6. Shepard as the wild card, the part-organic-part-machine is only referred to in the ending choices.
A Prothean super weapon is the one and only (new) plot point put forward in the entire game along with the convenient 'resolutions' of the Genophage and Geth-Quarian war.
The way I see the ME spectrum is like this, ME1 as the most pseudo-scientific (pseudo as in trying to ground everything in the reality of the ME universe), ME2 as the most science fictiony and ME3 as far into the realms of space-fantasy-opera-emotion.
My biggest issue with ME2 was the number of squadmates and having them all survive or all dead
I find the cameos or absence of the ME2 squad mates in ME3 to be criminal. You spend an entire game trying to recruit people for the fight against the Reapers and immediately ignore them in the 3rd because 'they could have died'?
Well, so could Shepard. I'd have given Miranda, Legion, Tali, Grunt and Mordin plot armor at the very least and have them be a bigger part of the 3rd game.