I'm pretty sure the story goes something like "Ah yes, "REAPERS". The immortal race of sentient starships allegedly waiting in dark space. We have dismissed that claim..."
"Holy crap! REAPERS!!!! Shepard save us!"
That's all I need to know. I decided to save the council in ME1 just so I can see the look on their faces in ME3.
I ended up hacking the config file of my game and changing much of the game dynamics. I like it a lot more now. You can change virtually every aspect of the AI behavior, weapon damage, magazine size, fire rate etc.
It's fun to just cheat at first and give your weapons huge damage but after that got old I actually enjoyed tuning the game to my preference.