I've only watched (not played) the synthesis and control endings, because I won't consider playing synthesis and my possible-control Shepard is still stuck in ME1. That said, I have yet more thoughts on Why Synthesis Is Problimatic behind the cut.
There's always been a huge issue of 'how' synthesis occurs, but it's so far-fetched there isn't really much point in discussing it. What's more disturbing are the implications, and that synthesis seems it was billed as the 'right' choice.
The Final Evolution. Maybe it's just my inner bio geek nattering on, here, but that idea of evolution as a ladder or straight path? That's absolute bullshit. Evolution is branching. It's a process, not an end. There is no finish line. That the StarChild thinks there is just underlines my hypothesis that Reapers Ain't Shit At Biology.
Moreover, being alive is change. Why would stopping it be a good thing? Why would you want the end point, if there was one?
Perhaps the StarChild is just bullshitting -- it certainly seems likely, given that the voice-over ending contradicts his point by suggesting that they'll find new life (life untouched by synthesis? or not?) and that they'll improve themselves (oops, more change! Must not have been final after all).
Mind control. I can deal with having the husks and reapers stop attacking. They received a signal which changed their programming, so they back off. When we do that to humans we call it 'mind control' or 'brainwashing', and it's bad, kids. The fact that the people locked in battle with husks are shown disengaging instead of pressing their advantage confirms that the synthesis beam manipulated them -- as it has to, because otherwise it wouldn't be able to achieve the stated end of everyone sitting around the campfire singing kumbayah. This has always been the biggest problem with synthesis; Utopia Through Uniformity and Utopia through Thought Control are both absolutely repellent concepts... as well as concepts the rest of the preceding trilogy can be seen to be arguing against.
EDI says she's alive. It's meant to be heartwarming. It kind of is heartwarming, because she's a human shape and a human voice, saying she's happy. But... we spent the last 1.9 games learning that synthetics, AIs, already were alive. That they already were their own unique 'people' worthy of respect. All of that is undone by making a biological/synthetic mish-mash into what makes EDI 'alive.'
Those of us opposed to the Joker/EDI ship have occasionally been told that we're hating on EDI. I'd point to this as another example of the contrary -- I actually liked EDI as a unique and different character, as an artificial intelligence, and anthropomorphizing her lessens that. The synthesis ending effectively has EDI say "I was not alive before," with the subtext of "I was not a person."
We still don't know what's actually going on. What does it mean to be partially synthetic? Clearly it's affecting the mind, or the kumbayah effect wouldn't happen. EDI is apparently partly biological, but... what parts? How do they effect her differently from programming? Does she have a liver? Just a few random chemical tubes?
Reapers share the knowledge of lost civilizations. This is the one thing that seems sorta cool! It ties back to the prior cycles and shows a gain, some benefit to this madness. And yet... are we to believe that the reapers have that knowledge because they're built through DNA slushies? That is not how DNA works. Did they record all that data electronically after more standard surveillance? If that's the case, why is 'being alive' necessary to access it? Are they compelled to share this mysterious knowledge through the same control the... what? Starchild? Harbinger? Shepard? exerts over humans?
Current hypothesis: What actually happens in synthesis is that space-magic installs some tech into the organic brains which allow StarChild to send orders to that tech. With the organics nicely assimilated, StarChild/Harbinger orders the reapers and organics to play nice. It's a control ending... just a different one.
TL;DR: Here's the new synthesis, same problems as the old synthesis. But at least the Normandy isn't stuck, yay!