I do love this trilogy but boy where do I start?
It doesn't make sense that humanity is in a 'golden age' so soon: expanding so fast, colonising so much, and improving its tech at an astronomical rate only twenty-something years after first contact. I call bull. This could have been explained if say, earth's climate was on the verge of collapse, or the remnants of nuclear war and environmental damage were making it un-liveable with its population; that would explain the investment in space travel pre-contact and the push to colonise different places, in preparation for an inevitable exodus of their homeworld. I would also like to add an extra thirty years at least since first contact and the events of ME3. More time would mean most generations would be well acquainted with alien contact and tech, and would also explain the Alliance's relatively high power as well.
On that topic, the amount of time between 1st contact and the events of ME make it highly unlikely that Alliance military would be so co-operative with aliens, especially as much as to let them on board. As it is, most soldiers above the age of 30 have some memory of the 1st contact war - and most high ranking military officials, the ones which Shep answers to, probably fought in it. It makes little sense for Shepard to let aliens on board a stealth alliance vessel given the tiny time gap (oh sure, it was co-built with the Turians, but I doubt the Alliance takes much notice of that). ME2 was particularly jarring in this regard - I mean, aliens on a Cerberus ship. I know old companions were meant to help Shepard adapt to the weirdness of the situation, but really I think Shepard is hardy enough that it wouldn't be too much of a concern. Especially with enough Jacob-types around her - level-headed, sceptical of Cerberus, etc.
I have big problems with the Lazarus Project/working with Cerberus in general for this reason. I don't like sudden revival as a trope - although the two year gap does make some ex-companion relationships quite interesting (Ashley, Kaidan, and Garrus in particular), it does mean killing off Shepard as a rule is quite cheap (and thus ME3's death ending doesn't work). I also find the idea of Shepard not having some kind of trauma or difficulty adapting back into military life is bizarre and unrealistic. I would have preferred that Shepard have been found alive, but in a coma. Of course, this means she could be treated in a conventional (if secret military) hospital and the tie-in with Cerberus is impossible. But even if Shepard had been revived by Cerberus, what's keeping s/he working for them? Why didn't they have the option of grabbing the first shuttle and run back to the Alliance? Or, if they'd been reluctant to comply, at least work this Collectors/Reapers situation out with her own ship, as part of an on-going Spectre investigation? Shepard has the authority and ability to build a crew, get a ship, and conduct an investigation from the beginning. I think it's very difficult to play an pro-alien Shep who sticks with Cerberus.
Cerberus, on that note, is overpowered and overfunded. Where does all this money come from? God knows. Apparently The Illusive Man is an ex-tycoon - although a personal fortune usually can't cover the start up costs of something like the Lazarus project and simultaneously fund a growing organisation. A former black ops with emphasis on scientific and tchnological research would not realistically have that many mooks to spare (unless they had some deep undercover cloning operation going on). Cerberus is blacklisted in a lot of space, and likely benefits from keeping stealth, so where would they keep them anyway? (Also, where would they get that much damned money if they were secret? The only way I can see it working is if they had strong links to pro-human supremacist groups on earth). Even then, I doubt a shadowy organisation would take such a risk with a pro-Alliance (or worse, pro-council) soldier like Shepard, who had alien associates, for their agenda - not for the amount Lazarus costed.
Suicide mission where nobody dies. I know this may be cruel of me, and unpopular with others, but I'd like one mandatory death please. I worked my arse off to ensure my team was loyal, and thus would survive, but it did feel quite empty when the only one who didn't survive my suicide mission was Kelly. Besides, ME2 has too many characters for its own good
(they're all great - but just too many to juggle for how few main missions there are).
Common complaint, but I don't like the direction they took with Liara. I like her character well enough, but not her role. From being an awkwardly forthright, bookish archaeologist who strongly dislikes all the corruption and secrecy on Noveria, to the Shadow Broker? Nah. Keep her as an archaeologist whose interest shifts towards identifying and looking up examples of Prothean-Reaper contact, late Prothean society, and Repaer tech. in general. That keeps her plot relevant. I think her confrontation with the Shadow Broker can still make sense from that angle - it's possible, given his contact with the reapers, that the SB is indoctrinated and using Reaper Tech. - Liara may recognise this and still try and track him down regardless of the fact that she is completely out of her league. The experience makes her more people-savvy, more cunning, more clever. and arguably the SB expects her to be more naive and foolish than she actually is, but doesn't turn her into some expert information broker when she's not a fan of large crowds. When she gets to the SB's lair, she shuts down the operation. Liara knows that it may have terrible consequences - but makes the decision either way. Keeping the LoSB plot means you get good development of Liara's character (and besides, it's a really great mission), but making her the Shadow Broker? Nah.
ME3 I actually liked for the most part. Still, I have four main problems with it - Cerberus is still overpowered, Kai Leng sucks, I hate forced multiplayer, and the endings. To expand on one of those: Kai Leng was annoying because of the lack of development in his character (asides from his obsession with killing Sheaprd), and the fact that he was basically unkillable until the very end. I wish Cerebrus had more minor villains for that purpose. had Kai Leng sacrificed himself to smuggle the VI out on Thessia, for instance, that was a trade-off that would have been satisfying.
ME endings were... ugh. The lack of a final confrontation with Harbinger annoyed me. The conversation with the Catalyst didn't have enough options where you could tell him that he was terrible, that these choices ****** sucked, that he had caused so much genocide for ****** nothing, that he had massively simplified synthetic-organic relations, and didn't go into detail about the kind of order the Reapers present, etc - basically, the lack of call-out options annoyed me. I don't see why synthetic-organic conflict was the core conflict going on for Catalyst - because, really, isn't ME about making difficult choices, sacrifices, to do what is necessary? or whether that's necessary at all - and arguing that there is another way after all? Isn't it about navigating messy, grey galactic politics when faced with a black and white, clear-cut, looming evil? Isn't it about finding a way to cut through those politics and tensions - whether paragon, renegade, or something between - a way to retain your resolve in the face of total terribleness? I would have liked the Reapers to remain some unconquerable big bad. I would have liked their motivations to be utterly atrocious, as seeing themselves as some self-righteous higher synthetic-organic solution rather than a total monstrosity. I would have liked the Catalyst to be called out as a machination of that terrible evil mess. Note: I'm a big fan of Indoctrination Theory, and whilst it's not canon at all, I'd honestly think it'd be a much better way of dealing with the ending, and deal with the themes of ME.
On the endings specifically: Synthesis was a total cop-out which relied on space magic and hopefully is never spoken of again.
Destroy, I have a few problems - why does it destroy all advanced tech? Like it's so arbitrary what counts as 'advanced'. Surely everyone would die if this was the case, I have no idea where you draw the line between machine, VI, shared networking AI like the geth, limited AI such as EDI in ME2, and 'true' AI such as EDI in ME3 and the pro-geth ending in ME3? If you put that line too low, suddenly mass effect relays are obsolete and people are stranded in universes without adequate resources. Explosions which destroy relays would destroy entire star systems - including Earth's. Why not just limit it to Reaper tech, which is synthetic-organic and uses elements of indoctrination? That makes far more sense. You kill off all the Reapers, their gooks, and anyone in the process of indoctrination. I could partially understand exhausting/destroying the relay network - and thus, most of the galaxy (although not all, since some require conventional FTL to get to a relay) - in order to kill the Reapers, thus putting civilisations thousands of years backwards. Like, that's the decision you make, and you make it knowing Earth is fried in that situation - but you do it knowing that the Reapers will never be back. Also, let's be honest, the chances of Shepard surviving that are nil.
Control, I actually quite like, if it's made more clear in the epilogue that it's a totally evil choice. Shepard becomes the secret Reaper Queen of the galaxy, and the cycle may continue under her reign. You gain the power to transcend indoctrination and instead, can only control others as a means of interacting with them - it's terrifying, regardless of your Shepard (honestly I think Paragons can transcend into lawful neutral at times, and could easily end up straying into a justicar-esque black/white mindset: bad when you have the ability to exterminate the galaxy). I also like IT's variation where you succumb to indoctrination under that choice, where the Catalyst is actually a piece of Reaper indoctrination tech. that is required to target the Reapers specifically, and choice is mostly in Shep's head, a hallucination to stop her activating the Crucible. I think given the costs of Destroy, it's an interesting alternative choice. You "live", and you save the present but ultimately sacrifice the future, because the Reapers are still living.
I also wish, given that it's the end of the series, we'd gotten some damn epilogue slides. I want to know what becomes of my crew - does Liara change the Shadow Broker into a force for good or does she crumble under the stress? Does Garrus become the next Primarch or end up going vigilante again? How does Wrex cope with having sixteen sons and daughters? What happens to Tuchunka, to Palaven, to Thessia, in turn? Does Cerberus crumble? What sort of galatic government is in tact? etc. etc. The voiceover we were given as part of the EC was not enough.