Why are those logistical problems? Why would any of those things change? You're still humanoid, you just have synthetic systems as well.
I don't see why the ending was expected to end all wars regardless -- it's not like people are magically going to be okay with past issues because the Reapers were killed off. The Reapers are no longer intent on destroying humanity but would rather coexist and benefit humanity because they have ties to them now.
You've prevented annihilation and created a temporary peace which is literally all that Shepard could have hoped or aimed for. Technology hasn't been wiped out completely, rather everyone has advanced. Win-win-win situation.
The synthesis ending has 2 possible mutually exclusive outcomes.
Outcome 1) Everybody changes in such a way that they are all homogenized beings against their will. People who weren't even in the war yet. Some pre-space -exploration culture just completely lost their free will and became cyborgs and are now forced to be all peaceful because the little vent god said it was the final stage of evolution. It's not much different than the ascension idea of turning people to goo and making them reapers. Forcing this orga-synthetic hybridness. (Notice the vent kid has happy names for horrible things? Ascension! Turn people to goo for reapers. Synthesis! Mutilate people and brainwash them to your will!
Outcome 2) Everybody simply gets wires and circuits, and nothing else changed. Nothing prevents orgasynths from creating fully synthetics. Plus people on pre-industrial worlds are like "What the fuck dude? where did all these wires come from? And why are they on my hat? So all it really accomplishes is forcing cosmetic changes on everybody, and freaking out the primitives. And if this is the case, why would the reapers stop?
Plus there's the stupidity of Green magic flowing through the galaxy GIVING PEOPLE AND HATS WIRES AND CIRCUITS! How the fuck does that make any sense???
I can't wrap my head around how the destroy option would be the best way.
I mean, we're all fans of Snake Plissken and Escape from L.A., but c'mon.
Dude! The whole game was the search to destroy the reapers! You wanted to destroy them from the start. Seriously. Reapers bad! It was the purpose of the game. Sadly the Geth are sacrificed to stop the Reapers! This brings back free choice back to the universe. Blue keeps the reapers, and umm I dunno, hope this control lasts more than 10 minutes after Shepard was vaporized. And the green ending: See above. to reiterate... REAPERS BAD!