According to the writer for Mass Effect 3, the original plans for the ending wasn't going to include making the same ending with 3 different colors or the current fan idea of the "indoctrination" theory but instead revolve the entire game around the issue of dark energy.
The 50,000 year cycle and real reason for Mass Relays would have been explained a lot better along with the small twist near the end of showing the Reapers were actually good guys.
The only thing that wouldn't have changed was the endings would still be triggered by a couple of choices and previous decisions made in the series had no impact.
http://www.giantbomb.com/mass-effect...rgy/35-540743/
http://www.strategyinformer.com/news...fect-3-endings