#1 The Reapers
according to ME3 they're conservationists and wiping out a couple of organic civilisations every 50k years is the best way to save all organic life from being killed off by some random synthetics.
i really, really would have prefered NO explanation to THAT explanation. final dialogue: "our origin doesn't concern you, neither does our motivation, you must only know this: you will be destroyed."
#2 Starchild
everything that needs to be said about this boy/AIs tale, has already been said. my opinion concerning his appearance: hudson & co had sentient starships that are 2km long and ancient-beyond-measure at hand, but they chose to confront us with the hologram of a little boy.
f*** starchild, give me harbinger, this feels like return of the jedi without darth vader, the emperor AND the death star.
#3 The Meaning of Life
the should have let my decisions matter until the end. i appreciate how the game resolves issues like the genophage and the geth-quarian conflict, but during the end, nothing matters. i'm not talking about a dozen different endings, i only want two: fail & suceeed, but very much like the suicide mission from mass effect 2, i would like to have had my version orchestrated in a more or less unique way. all available crewmembers should have been in the fight at the the end. different squads, different tasks. volus bomber fleets and shadow broker squads (for instance) to help them, if the player accomplished the side quests.
the last part's much too linerar for my ME taste.
#4 A, B or C?
bech. 'nuff said.
back to #2. final confrontation with harbinger. he's trying to assume control and depending on stuff that i did during the campaign i'm given more or less options to fight this, finally resulting in either a) becoming indoctrinated by harbinger and deactivating the crucible or

resisting the old fart and pressing that bit red button (i'm sure buttons are univeral tools to activate things - unlike reaching into lightning or shooting pipes) and destroying the reapers. if the player didn't collect x amounts of scientists this also destroys the crucible/citadel, because a couple of screws were loose.