There were many things wrong with Mass Effect 3 - the biggest one of them being that the writers chose to abandon the storyline set out by the lead architect of this series.
TBF, Drew himself has said on many occasions that they never had the dark energy storyline nailed down. It was one of a number of endings that they were considering. It was dropped late in the development cycle for ME2, only it was too late to take out the references to it.
Even had they gone down the DE route then you'd still likely have had similar problems. You would have faced the moral quandary, and you'd have had someone like Starbrat giving you the choice.
Unfortunately the DE plot was never fully fleshed out, hence we'll never know whether or not it would actually have been any better than what we got.