Yes, we don't know much about Synthesis. But we don't see any downsides in the slides, so I have to work with the information I'm given rather than concocting or supposing unsupported hypothetical downsides in the appearance of an argument against.
Here’s a problem; we don’t know of any upside either; at least not for the individual. And actually, if you notice, I did work with the information provided by the game, plus knowledge of human nature including as it is shown in the series.
Synthesis is the answer to a specific problem. Not a form to satisfy the needs and desires of the individual affected by it. That is one of the few things that the Catalyst does tell us about it. It is an imposed transformation to satisfy a debatable need external to the individual.
Plus, ME humans being human, it is expectable they react as humans do; unless the story provides a clear, valid reason why it is not so; in this case, I would argue that to transform someone to some degree without their consent, (and arguably for a dubious reason to boot), it is likely to create an adverse reaction of many of those so transformed.
The "correction" of organic flaws may well be irrelevant to the Shepard deciding. The decision that Synthesis is the best choice need not include the decision that organic/synthetic relations are doomed, but rather that this is the best way to stop the Reapers. Now, the fact that the Reapers are still alive and well is likely to cause a great amount of confusion and turmoil in the years to follow. But the game implies through the slides that eventually peaceful coexistence prevails, at least to the same degree that such prevails among any of the galaxy's inhabitants (which is to say, intermittently).
I believe that is reasonably expectable that a good part of the population would not embrace synthesis, or the Reapers, as it seems to go against human nature to expect near unanimous acceptance of a rather invasive transformation, performed for nebulous reasons, at the behest of a rather heinous enemy.
Now, if the writer decides that humans, (and aliens), will react, in this instance, in a way that is not reasonably expectable by a good part of his audience, (as it seems to be the case), then he should provide a clear reason why is it so.
To not do so means his writing fails, as the believability of the scenario he created is broken. It is not enough to produce EDI claiming she is enjoying her new situation, plus a bunch of vague expectations she may have of a bright future, or a number of generic slides, coloured green, that provide no information about the why is it so, as it fails to provide a reasonable reason of why it is “so good” a solution in the first place.