Almost the entire series consists of "space magic" as in stuff that makes no scientific sense (this relay lets you teleport your mako directly on the citadel presidium; People are being molten into grey goo and then somehow form a new entity in the shape of a Reaper. Braindead Shepard gets revived somehow; Blue space chicks can somehow have children with every member of other species no matter if male of female; And even in a society that consists of multiple species where multiple ones are way more advanced than humanity humans are still somehow the most awesome because f*ck yeah humans....Äh I mean genetic diversity or some such BS).
But Synthesis is widely hated by the BSN community, thus it gets called out for being space magic more often.
The difference is that everything you mentioned was given some explanation in the lore that fit.
The relays use element zero. The prothean's making a precise relay isn't improbable because ME2 shows us that you CAN refine the transit to be more precise without crazy drift.
There is all kinds of lore supporting the goo being possible in the ME universe.
Asari are explained in the codex and in the dialogue with Liara. It isn't as nonsensical as you make it out to be. Also, technically, they don't have children with others. They use their own DNA, none of the fathers genes are actually used. The mother is always the sole parent of the child. Hence why its possible in the first place. It isn't like their womb just accepts all types of seed for some reason or another. They don't produce the same way we do, they're alien.
Reviving Shepard wasn't perfect but at least it does have some bases in the lore.
A species being advanced technologically has little bases on their genetic diversity.
I just can't see it as fair to compare the space magic of synthesis with anything else presented in the lore. It's leagues above all the rest in terms of stretching belief.
Where does it say you're replaced with "synthetic" DNA? Only says our DNA will be changed.
Not necessarily replaced but rather merged. All life becomes one, synthetic and organic. We all have the same techo-dabbed DNA. Which technically would make everyone and everything, even plants, synthetic.
That's speculation that I believe a lot of people got wrong. When it comes to what the Catalyst says, he only mentions the beam changing our framework into a new DNA, and how we'll be better integrated with technology. He never says I'll magically have robot parts put into everyone, and Extended Cut slides kind of prove that didn't happen.
Did we watch the same ending? It's on youtube, you know. It isn't speculation. I'm not assuming thats what happens. I'm just parroting what was told to us by the catalyst and EDI. As for for not magically having robot parts put into everyone... again, did we watch the same ending? We totally see that. Everyone has green circuit lights all over their skin, even the leafs on trees. The DNA strands even have techno magic junk merged around them. This isn't speculation, its synthesis as it stands. If it was just speculation it wouldn't be such a problem in the first place. You can ignore speculation - you cannot ignore whats real.
We're all one, synthetic and organic, merged together. There are no more borders between us. No more fighting or violence. Its a complete utopia where everyone is one. This isn't my my speculation, its what EDI tells us. It is lore.
Like I said, the only time the Catalyst talks about how it'll effect both in general, it mentions a new DNA. It never says we'll get augmented by beam, but will be integrated with technology, which can mean anything really. I can be integrated better with my phone by just attaching it into my watch.
Catalyst and Edi says we all changed. Never did they say we all changed the same way, or in what way beyond "DNA", and somehow this allows us to be better integrated with Technology. Does that mean my DNA is the same as an Asari now? No. That's speculation. Saying we did change the same way or changed in different ways is unknown. We only know, based on what EDI says, is that we're been "changed". Changed into what exactly? Never explained beyond DNA.
It says we'd all have a new framework and dna. Synthetic and organic life will be combined. Anyone who watched the ending should know this is lightyears away from being like attaching a phone to a watch. If it was that simple I doubt you would have as many people, even Shepard, arguing against it on a moral standpoint.
It does say we changed the same. We all have a new framework built upon the merger of synthetic and organic dna. It is the final evolution of life. There are no more lines. No more divisions. We are all one. Thanks to Organic-Synthetic Shepard jumping into a beam of light that triggered a chain-reaction that causes all life in the galaxy, organic and synthetic, to all become one new framework, a new form of life. There are no longer synthetics and organics. The line disappeared. We are all one now.
Keep in mind also that in Extended Cut, even after learning who the Leviathans are, you can ask who made the Catatyst, and it will dodge the question. It'll only mention Leviathans if you bring them up specifically. Leviathan's know nothing about about the Crucible is your speculation. Leviathans themselves say, after looking down and thinking of what to say: "We've watched its construction before. It has never been completed. Those who have tried still fell victim to the harvest. Its outcome is unknown." So yes, they do know about it. And if they had, it's possible they might've messed with the designers of it. The designers being someone "We don't know them, and there's not enough time to explain". My speculation. 
You're taking me out of context. I explicitly said that they knew of its construction. When I said they don't know about it I meant they don't know its function or design. They know OF it but thats it. In the same sense Javik 'knew' of the crucible. You're pointing out a piece of the lore that I myself already recited to you, as if I don't already know that.
"They didn't know anything about it, except that its been constructed before but never succeeded. The catalyst also points out we would not know the creators, while it knows we met the Leviathans."
You also bring up the catalyst dodging the question even if you know who the Leviathans are. I know that, I'm just surprise you think it actually favors your speculation. Imo, the fact that the catalyst says you don't know them even though it knows you know Leviathan should prove that Leviathan didn't create the crucible. My view is based on lore, what is told to us. Yours is speculation. Which is fine, just don't accuse me of being the one making up speculation when everything I mention is in the lore.
Altering minds is also suggested if Wreav is in icharge of teh krogans, they do not go to war. Like I said, it may seem benign, but there's some ugly implications about that.
Personally, and here comes my speculation, it isn't so much that their minds are altered but rather they're suddenly given metric tons of knowledge. It's like a caveman getting a ton of knowledge suddenly beamed into his head.
Depends if Shepard being more synthetic with all the Cerberus cybernetics really matters. Or if being alive matters. Or if non reaper tech matters. I mean, you could say the same about Tim's dead body.
I agree with that.
Something to consider about TIM. With TIM, it wasn't really synthesis. Just as it wasn't with Saren. They did not work together as one, he was just a tool, a puppet to the tech. There was a power struggle between what the organic wanted and what the tech commanded. Shepard is different. Shepard /is/ synthesis. His body is like 30% synthetic but yet he's embraced it and the organic and synthetic bits all work flawless together. There is no struggle for control, its just a part of him. He is Adam Jensen.