You forgot to mention an intricately thought out universe that is far harder sci fi than is the norm in games (the ending notwithstanding).
The hardness was always a bit spotty. On the one hand the gates were well explained (for a video game) and a lot of thought had gone into the different cultures and how they became like they were. On the other hand it's full of humanoid aliens that can have sex with each other, all the powers are always given a very BS excuse for existing (Which is always 'it works with the mass effect.' Including being able to drain someones life force and increase your own (or drain their barriers and fix your own). It's got very detailed explanations of how space battles work, but on the other hand it completely ignores them right from the get go and the space battle in ME 1 had people firing from ramming range and a bunch of frigates getting a killing shot on a destroyer. Cerberus mad science etc
If the universe was in fact, harder sci fi than the norm in games (which it really isn't since the entirety of the game's main scientific achievement, isn't - because any idiot can take element zero and run an electric current through it), then we could reasonably some degree of intelligence.
There isn't.
Geth vs Quarian - Quarians started firing on the Geth because the Geth started becoming something more, which frightened them. Thus the Morning War was born, and from there, nobody thought to wonder why the Geth only kicked the Quarians off Rannoch and NOT why the Geth didn't simply run after the Migrant Fleet and gun them down with both superior numbers and firepower.
Citadel - Quarian relations : The Quarians created the Geth, whom after defending themselves, went and isolated themselves until a sect of themselves were corrupted by Reapers. Nobody asked them for their side for over 300 years. Instead, the development of all artificial intelligence is banned and considered a crime, and for their trouble, instead of being given help to recover, the Quarians are subsequently kicked out of the Citadel Council and left to rot for 300 years.
Krogan: Pre-FTL civilization uplifted by the Salarians to fight the Rachni for them because of their ability to survive in harsh environments. Once the war was over and the Krogan started going out of control, instead of properly dealing with it, they cursed the Krogan with the genophage and sat back while they tore themselves apart.
Rachni: The reason Krogans were uplifted due to their ability to survive in harsh environments. What the hell are hard suits made for?
Let's not forget the biggest offense:
Protheans: Believed to be the builders of the Mass Relays and the Citadel - except there is little to no evidence (EXCEPT THE RELAYS AND THE CITADEL) that anything besides the Protheans existed 50,000 years ago. Apparently, nobody's heard of radiometric dating. Let's not forget the Mars Archive and the Beacon on Thessia which the Asari have been hoarding all those years to advance their own "technology" above other races.
For a game attempting to be science fiction, it fails at its own genre.
Addendum to previous comment : It appears that AI research was banned before the Geth, though the Geth are used as the AI "boogeyman" afterwards. Regardless, the argument stands.
It doesn't fail at it's own genre because science fiction doesn't have to be hard and some of the best of it wasn't. And even with hardness as a factor, it's the softness that allows writers to really explore the medium. The cool thing about Asimov is a mixture of him predicting the rise of dependence on machinery but exploring that sort of relationship with the gobbledy gook 'positronic brain'
But as another example you reminded me of, throughout the entire series, including 1. AI has stood in for 'magic people creators' instead of anything an AI would actually look like. It's full of AI's going rogue and robot fighters that don't have machine precision etc... ME 3 was of course the worst with the magic reaper code (that contradicts the Geth specifically denying Reaper code help in ME 2 because outside inteference removes their ability to self-determinate as a species). And since ME 2 they've had the idea that if you grind someone up and turn their lumps into circuitry and that circuitry into a spaceship (and make that spaceship the same shape as the animal, but 100x larger with some extra eyes) something special happens.
And that's not how science, people, consciousness, spaceships or circuitry work. From what we've since learnt, from the very beginning of the series hardness in terms of villains was never even close to being on the table
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Would've been fine, had it not been for a few things
Good things about Mass Effect; On the surface, it's a story about underdog humanity trying to make a place for itself in a space dominated by alien species. Humanity is new, and is seen as an outsider moving up the ladder far too fast. *SPOILER WARNING* This of course later on becomes a plot point when you get arrested and wind up having to save the very galaxy whose governing body essentially did to you what they did to the Krogan - uplift, then knock down.
Bad:
Start digging a little deeper, and the game world begins to warp. Some of this is due to the gameplay changes between ME 1 and 2, such as the addition of thermal clips. When you consider the reason for moving to thermal chips was because research showed that the one who could put the most rounds downrange faster, won, was something they got from the Geth, you have wonder exactly what kind of thought process they're using here. Consider this - the Geth, being machines, can perform repetitious tasks with far greater precision and speed than an "organic", and as such, can swap out thermal clips from their weapons much faster than any organic.
The other issue is that the whole reason for the Reapers seem to be born from another debate regarding how artificial intelligence and bio-organisms exist, co-exist or don't. It gets even more convoluted when you consider the original reason for the Reapers' existence was because a species of gigantic organisms (Leviathan) tried to find a way to stop the civilizations that paid them tribute from destroying themselves all the time by creating an AI to figure out the answer. The AI's answer is to eliminate all live past a certain point of technology every fifty thousand years. And, the reason these faces kept killing themselves was because they kept developing "synthetics".
See the irony? The game revolves around a superior race trying to stop lesser races from annihilating themselves through the creation of artificial intelligence and life forms, by creating an artificial intelligence to figure out the answer.
If you're looking for gameplay and character development, great. If you're looking for anything deeper than that, the game fails the mark. Badly.