I only read the OP, but I had the same impression as you regarding the ending with Synthesis. I didn't like that ending, even though I chose it the first time I played it.
The second time, after learning all about the Indoctrination Theory and hearing everyone's reasoning on which endings are best, I chose Destroy and got the "Shepard Lives" ending. Everything fit so much better. The scene where Liara doesn't put your name on the wall cause she knows your alive was touching to me in a similar way as her Final Gift scene. During Hacket's speech, the Citadel is shown to be reconstructed, and life seems to be back to normal.
The Destroy ending gave me peace, whereas Synthesis left me feeling that I had made the wrong choice. You may want to give that a try.
Regarding the Catalyst - its purpose was never to destroy all organic life, nor to preserve existing organic life by destroying synthetics. If you pay attention to what it says, its idea is to prevent other synthetics from "going rogue" and killing ALL organic life in the galaxy, completely exterminating it. Its only goal is to keep organics from hurting themselves by harvesting them before they create an AI worse than the reapers.
In other words, the reapers are bad AI, but they have a cap that prevents them from killing off organics completely - they allow some life to continue. Their purpose is to prevent the rise of synthetics that will kill without that cap, and therefore save organics from their own creations. It makes sense from the perspective of an unfeeling AI, whereas we put a lot of emotion into the idea of synthetics killing civilizations off every 50,000 years. That's why the Reapers always talk about being our "salvation through destruction". The Catalyst see us as children who, at roughly every 50,000 years, are about to step into an oncoming train's path. It sees the Reapers as the guardian trying to save that child. Its reasoning is, in a way, logical; however, its solution is completely unethical.
With this in mind, I don't have a problem with ME3's ending. I actually kind of like it. And this is how I sum up the three choices:
1.) If I choose Destroy, I'm doing so knowing that Shepard just stopped a war between the Geth and the Quarians, and knowing that my Shepard's relationship with Legion and EDI prove that the Catalyst's assumption that synthetics will always kill organics is wrong. This cycle proved it wrong, and by wiping out the Reapers, the Geth and EDI together, I'm starting over with a clean slate with which I can prove the Catalyst is wrong.
2.) If I choose Synthesis, I am stating that the Catalyst is right, that there will always be that conflict. By combining organic and synthetic life, I am going to prevent it.
3.) If I choose Control, it is with a similar mindset of Destroy. However, the ending is unknown. On one hand, the Geth and Edi are preserved, which makes Shepard's personal sacrifice worth it. However, we do not know if Shepard will eventually lose control, or be swayed to the opinion of the Catalyst, and unleash the Reapers on the galaxy once again.
For me, Destroy satisfied me most. Hope this helps you (and others) see the endings with a different perspective.