It's quite ingenious really.
For example, the synthesis ending is a direct point to Clarke's third law. The player has the choice therefore to reject this law and thus reject that the Reapers are gods.
The destruction ending is a direct commentary by Walters on OSC's view of gay marriage. By showing the destruction of geth, he is obviously representing homophobia in the sense that the Geth, or synthetics in general, will never get along with organics.
Control is obviously a dialogue on the 'Three Laws'. Since the Reapers don't obey these laws, the player as Shepard can thus enforce these laws on the lawless Reapers. It's trying to adapt these foreign Reapers into a set of laws that can be used to govern their current actions. This way the Reapers can be properly instituted into society as people can depend on them.
So in the end the player is choosing their perceptions of classical science fiction authors and which direction they want to take the universe. One full of magic, one with discrimination and one that is traditional. It's very meta but still very genius.