Things you wish would've happened in the trilogy

No because we have no clue what Shepard will do as the new Catalyst aside from "Helping the many" or something. When he's renegade it's heavily implied he will be a dictator however. If you have only Wreav, no Eve and cured the Genophage he will say something about keeping the aggressors in check when necessary as it pans over the respective slide.

The main point of my calling it self-sacrificing for the greater good is due to the arbitrary and tired "synthetics vs organics" thing. I'm judging it based on what I think the developers put into the choice. They meant to say that Shepard continues the cycle and tries to see if he can find a better solution to the potential genocide caused by synthetics/organic wars than to automatically kill people every 50k years as a safety precaution and thus sustaining the cycle in some fashion as opposed to not believing that there is a danger and potentially leaving everyone to die by picking destroy (and EDI and the Geth of course), just so he can get things to be the way they used to in blissful ignorance of the future.

The Reapers are meant to prove that there is something out there that's beyond the scope the average organic can comprehend and so they're our safeguards. Neglecting them that role by destroying them and all other synthetics is to condemn the galaxy for a self-gratifying fix. I was always against the whole "Wow, BioWare switched the morality alignment to confuse us with the destroy and control endings!". No they didn't. Red is destroy because destroy is the narrow-minded, shortsighted and selfish decision.