The idea of combining the two forms of life would be that there would be no need for either organics or synthetics in the future because there is a new form of life that is superior to both. They are intelligent and computational enough to produce new types of bio-synthetics like themselves instead of reverting to purely synthetic beings due to knowledge of their shortcomings. Also you don't know that they will be different people. Joker and EDI seem to maintain the same relationship so you'd imagine they are the same people.
First, it is only "superior" on the word of the being whose idea of helping organics was killing all advanced civilizaitons every 50000 years. So his opinion is already on the laughable side. Second, I don't see how you can say they are the same when you start listing all these things that are better about them. Will Krogans still be war like and jerks, or will their new superiorness make them not so? Will the Hanar no longer worship the Protheans? Will the remaining cerberus people still hate non humans?
And what is this creating new types of Bio-synthetic? Since you enjoy taking the word of the Catalyst, this will still cause war as if they create new biosynthetics, because as he said, the created will always rebel against their creators.
Rewriting someone's DNA to be superior is not the same as drugging people to be peaceful. The bio-synthetics would not be forced to be peaceful by way of their nature, rather they have the perfect balance of instinct and intelligence to know that chaos is counter-productive to their ends. The reapers never gave them a choice and provided the galaxy terror with no end. Shepard only gives no choice when it comes to a far more harmonious option.
Rewriting their DNA is actually worse than drugging, drugging could be stopped. And umm that is what I meant by forced to be peaceful. They, against their will, were forced this change upon them, and the changed self is Peaceful by its nature. And if it wasn't peaceful before, and suddenly it is, it was changed on a fundamental level. How can a person who was warlike and a dick before, and suddenly not anymore thanks to synthesis not count as changing them as a person? Just because you like the new person better, doesn't make it right. It's still a form of brainwashing, only it's worse because it's changing their very nature.
The thing is, you still have no proof about how these people will act and you refuse to consider the idea that this new type of life that is ideally superior to either previous forms would be in the best interest of every being. We weren't given a choice to be born into the universe but it still happened. What exactly is so horrifying about being born into better circumstances?
Let me answer your question with a question. If you had a kid, and I broke into your home stole your child, then gave him/her to a family much better off than you, would you be happy with that? I mean, your kids life was better than you could have made it, right?
You don't think it's hell for those in existence? You just spent the entire game watching refugees lose their entire families, people watch their neighbors become mindless husks, and entire worlds catch fire. How is this not the most terrifying and painful way of change imaginable? So your logic is "oh no they forced a completely zen, celestial, and merciful rebirth of all life in the universe" is much more evil than "here come those giant mechanical death-lords to take away the life and free will of everyone you know and love"?
It's worse to me looking in from the outside actually. At least the reapers let people advance to a certain point, and even gave them a fighting chance. They had hope. You aren't even giving them that. You just change them. And sure, if I was in the situation, I wouldn't even know the difference. I'd be living my life and one day BAM I'd be completely different, and worse, I wouldn't even mind because my very nature was altered. Let me tell you something: I DON'T WANT TO BE BRAINWASHED. No matter how much better and superior YOU think it makes me. That's the whole deal. You are deciding for the entire galaxy that this is better. I would like to keep my "very nature" the way it is.
Killing all synthetics wouldn't stop the future chaos of organics vs. synthetics. Except then you'd have nothing like the reapers or bio-synthetics to keep things in check. You'd just have more war. The green option is the absolute best option for existing organics and synthetics. It's painless and beneficial to all life in the galaxy.
Once again you follow the Catalyst's ideas blindly. Shepard made peace between the Geth and the Quarians. Shepard is all buddy buddy with EDI. Obviously the catalyst's logic isn't 100% perfect. Though, of course we already knew it wasn't 100% perfect. His solution to his perceived idea of Created vs Creator was to brutally murder people throughout the galaxy, and doing all those hellish things you posted before every 50000 years. So, sorry if I don't take his word that its inevitable.
And again, no thanks to the painless solution of brainwashing everybody to be peaceful.
How about getting rid of the reapers and letting the galaxy make its own choices? We didn't ask for the Catalyst to "keep us in check."