No, it was just like that: pick up a color and die. Even more so pre EC.
You become as good as no explanation from a character coming out of nowhere, self proclaiming itself as the Reaper boss, telling you that if the Reapers don't kill you every 50,000 years you'd end up killed off by your own robots. ALL of us. It is inevitable. Organics and robots can't coexist. Never. He knows it because reasons. So deal with it, screw the galaxy up in red, blue or green and just die already.
If you think the difference between the variations of the destroy ending depending on your EMS was just a color, you're not looking hard enough. Or haven't put much thought into it.
Reaper motives aren't anything like you mentioned. It wasn't about Reapers came here to kill you every 50,000 years so you won't be killed by robots.
They are here to only harvest advanced organics and preserve them into Reapers. They leave the lesser, primitive organics alone. The little kid tells you as much if you listen to what he says. Every day citizens were being turned into Reaper foot soldiers. You had a conversation with Tali about this. Or at least I did in my playthrough.
Those who cooperate with the Reapers are spared from harvesting, but are used as slave labor instead. They aren't let go to co-exist peacefully. The codex explicitly tells you this. Saren tells you this in ME1. Surrender (and be used as slave under Reaper control) or death (harvested and turned into a Reaper). There are no other options.
This was mentioned by Vigil in the first game as well. Some worlds were harvested; others were enslaved under Reaper control.
As far as convincing the Reapers. You couldn't convince the Rannoch Reaper that organics and synthetics can co-exist, at full health and clear thinking. I doubt you could convince the little kid of this being mortally wounded, confused, and near death.
If people think Shepard is going to have a conversation for 20 minutes with the kid and somehow convince him (if EMS is high), that wasn't going to happen.
In reality, he is near death and not all there. He is very much in-character for that scene.
At the end of the day, if it still bothers you, I would just put this game away and find a better one to play.
Ending wasn't going to change or be retconned in any way. Bioware stuck to their guns despite their fanbase still being upset about the ending for over 3 years. Takes a lot of guts to do that. For that, I applaud them.