Okay to respond directly to those points in as much an order I can keep.
[spoiler]Their leader is maybe an AI but seemed to respond more like a VI who was certainly at least designed by super advanced synthetics long enough ago to see the cycle enough times for the zetafuck of beings reaped before the current one who was very set in its programmed parameters.
I guess you like MGS storytelling maybe but I rather assume he knows his shit based off that than get an hour of exposition on why the war is inevitable and why he wouldn't take any of Shepard's shit. As for killing the reapers without it? Even if they didn't have a pretty good resource of examples as to why that's a fuck all terrible idea, by the time you could make the decision everything was on the line, there was no regrouping from that fight.
As for the final evolution guaranteeing peace? It doesn't. It just means it would be impossible for organics or synthetics to be wiped out since everyone is both.
Again for destroying all synthetic life I'm sticking with "I believe that's the only way it can work". A lame excuse, but since your complaint is "I don't believe that's the only way it would work", well, fuck you if you try to call me on it.[/spoiler]
That all said, the endings really could be a lot better without changing the themes drastically.
[spoiler] just don't destroy the relay with the blue pulse. Now people aren't trying to awkwardly fit "good" and "bad" labels but you have exactly what they're called in game
Break the Cycle - destroy all reapers and everything based on their technology (everything). Hope that shit never happens again, and if you're bad ass enough, even go home to fuck your girlfriend again. Well, someone else's girlfriend. Yours is now stuck on a deserted planet in a universe without faster than light travel.
Control the Cycle - Civilization gets to continue down the path it has been, everyone you know and love is still alive and mostly happy. The galaxy can start to rebuild and move on since you saved it from the biggest threat to ever face it, and now control that ultimate force. Civilization gets to continue down the path it has been, everyone you know and love is still alive and mostly happy. Whatever space may try to throw at life, organic or synthetic, you'll be their to stop it. You are ten thousand Godzillas.
Fuck That I'm Shepard - You inspire people so powerfully through charm or raw intimidation that nothing can stop you. By destroying everything that ever is, was, or has been Shepard, you're able to alter the genetics of all known life so it does what the fuck you say for the rest of eternity.[/spoiler]