I don't see how changing publishers between the first two games could account for them forgetting that they had to tell a story in three parts across three games. They very clearly never had a plan for the story of the trilogy or each game in mind before they were making the subsequent games. I don't see what EA or multiplayer in ME3 have to do with that. The writers of ME2 and ME3 weren't preoccupied with multiplayer when they were writing those games.
Expanding the audience and improving accessibility could be blamed for streamlining the RPG elements and having action based combat but that might not even be a bad thing given how poor and shallow the RPG elements were to begin with and how unfun the initial combat was.
The writing, you're right, that's on BioWare.
Science fiction is just a setting. It doesn't have different rules from other settings. Writing is writing. Things can be unknowable in sci-fi just as easily as in any other genre/setting. If The Sopranos can end by suddenly cutting to black then the Reapers can be ambiguous and unknowable.
Even if they hadn't already pulled away a lot of the mystery in ME1 and then went further in ME2, I still would think that if you're going to spend three games on an antagonist there should be a revelation of a motive for them.
ME3 is more of a statement about the importance of execution and not delivering a poorly written and presented reveal.
Other works such as Revelation Space, Xeelee Sequence, and even the anime Gurren Lagaan (lol) managed to have antagonists that weren't as botched as Mass Effect.
Although if BioWare was really gutsy and the narrative had you losing in ME3 (as the galaxy probably should) I would be fine with you never knowing.