The biblical references at the end of Mass Effect 3 are laid on pretty thick and i feel should be further explored. I realize there are about 10,000 threads about the ending to mass effect here so i hope i can offer a more unique perspective that warrants the creation of this topic.
The Grey area of Mass Effect is that no one character is inherently evil. The Reapers only want to destroy life so it can continue, the illusive man only wishes to secure humanity's future and organic life is ultimately interested in self preservation. (the genophage, the geth, destroying the Reapers ect) remember the quote “The Road To Hell is Paved in Good Intentions”
which brings us to the biblical nature of Mass Effects ending. Shepard is raised to the Heavens where she/he apparently meets God. God Tells shepard without his influence the universe would destroy itself.. So like in the bible where God floods the earth for 40 days and 40 nights because mankind has become so corrupted with sin it need to rebooted in a way. God has no faith that mankind would overcome its struggles and decides it better to start over rather then allow the scenario to play out. The Reapers do the same thing. Every 50,000 years the Reapers come and “flood” the universe so life can continue.
Shepard is the first organic to reach the top of the citadel thus God’s plan has failed (God has been proven wrong) and decides that maybe Organic life should be given a choice rather than its fate decided for them. depending on what you choose at the end the same bottom line happens. you either choose to Become God (control) Merge with God (synthesis) or kill God (chaos) Either way you are now removing God from the equation of life. Now Organics are truly the masters of their own destiny. you have now truly removed fate. The Mass Relays are destroyed, this further shows that Organics are now in the drivers seat. divine intervention no longer exists. if man wants to travel the stars again it has to do so on its own.
Furthermore when we cut to the Normandy, that has crash landed on a tropical paradise. the same thing always happens. Both Joker and a Female stand next to one another over looking their new kingdom. Joker and the female are now Adam and Eve. Ready to start life over again, but this time on mankind's own terms. The final piece of the puzzle is the star gazer ending. Which shows Organics are now in direct control over their own fate. anything you want awaits you out in the stars, no guiding hand, no intervention. Shepard is even referred to as “the Shepherd”
This by no means gives any “closure” to the narrative side of Mass Effect, but more goes in line with a overarching theme in Mass Effect. Freedom. Every race in the game wants to be its own Master The Geth want to be free of their creators, the Krogan want to be free of the genophage, the humans want to be free of their self induced oppression and so on and so on. Even, you, the player wants to be his or her own master in the choices the game provides you with.
Thats what i took away from ending of Mass Effect.
Edit. i wrote this in google docs, so sorry for the formatting...