My perspective on the three endings:
Control Ending (Blue): This ending felt like a bad choice for Shepard. To use it would kill Shepard with only time for one command to be issued. At that, there was no guarentee that the Reapers would not be back at some undefined future date. The Geth and EDI was going with the Reapers. What would they be like if they returned?
Destroy Ending (Red): This one is a reasonable answer as Shepard has orders to destroy the Reapers at all costs. It even has an off chance for Shepard to live.
I acknowledge this could be the best choice if the Reapers were still trying to indoctrinate Shepard.
There are three down sides to this choice:
--The first downside is the destruction of allied Geth as collateral damage. Destroying the Geth felt wrong in that they seemed like children rejected by their parents during the Quarian / Geth War. All the Geth wanted was to be accepted for what they were.
--The second downside is the destruction of EDI as collateral damage. I have to admit that the final conversation with EDI at the Forward Operating Base in London made this choice even more difficult for me. I figure EDI was as close to a daughter as Shepard would ever know.
-The third downside was that successive organic generations might repeat the past when they get around to creating the next AI race.
Synthesis Ending (Green): I consider this the Peacemaker ending. It appears to be the ultimate compromise, combining Organic and AI parts into a new lifeform based on Shepard. This new lifeform supposedly would not need to make war between Organic and AI as it had elements of both. Note, the new lifeform appeared to maintain its former general appearance instead of that of a Reaper.
Downsides include:
--A major lack of trust makes this a difficult choice. After all, Shepard has to die to make this happen. Why couldn't they just take a DNA sample? So much for the highly advanced tech of the Reapers...
--Shepard's experiences with other Reaper ideas of acencion further alienate this plan.
As for the destruction of the Jump Relays destroying their star systems in all three endings, a thought:
It appears that the relays were treated as shape charges exploding in one primary direction to set off the next relay. Heaven help anything in that direction, but damage is significantly less in all other directions.