The reapers were always designed as having an ulterior "good" goal. Drew's first idea was to have it somewhat related with dark energy. And they are not incoherent at all.
Were they? I heard about that dark energy idea, but I've no idea whether it was necessarily a "good goal" or purely a matter of self-preservation.
If their purpose was good from the beggining, then they simply ****ed it up from the beginning, because throughout the game they are constantly portrayed as malevolent pricks.
We had to kill organic life to save it.
Nope, not incoherent.
"We kill some organics to prevent the possible extermination of all organics" is less catchy, but more true. And in fact, it wouldn't be incoherent at all if it weren't for the simple fact that it's stupid, while the creators of the Reapers should supposedly be smart.
But whatever. I understand how irritating can beating the dead horse be to all the been-there-done-that people here, and admittedly it doesn't serve a purpose other than to vent one's frustration so perhaps it is better not to pursue it further.
So, on a brighter note, I did enjoy the game, and although I was never a big fan of Mass Effect, I must say that it felt nice to play ME3 (and ME2 before it, because I lost the saves, and the default profile was horrible). Those characters do grow on you. Especially since Mordin, Legion and Wrex had important roles in the sequel, while, say, Miranda, Jacob or Ashley did not

Also, I played the Adept, and what they've done with that class in ME3 is a vast improvement over ME2.