Myself, I would've liked a slightly altered dark energy finale where the Reapers always fix the dark energy problem every 50,000 year's but to fuel them they need to harvest organics. The problem is that in the Reapers minds they see the harvest as the important thing not fixing dark energy affected stars, although they do in fact fix the stars.
Then during the third game your mission is to fix the Reapers mindset which has become faulty and also to find a fuel source for them or indeed sacrifice organics if you failed in that. All the while the Reapers fighting you coz they feel everything is working well.
If I were to alter the actual ending as it is, I wouldn't give anyone a choice at the end, but have things happen in accordance with ur paragon points etc paragon = blue ending, middle ground = green etc. That might've been a more acceptable way of finishing this ending off.