There is a loss of individuality. Hell, even in Control, there is at least a loss of freedom - most of the known galaxy's individuals can be understood to want the Reapers destroyed, yet here they are. Synthesis takes that further, but also focuses on the loss of individuality, while seemingly granting a 'different' kind of freedom (the one to evolve faster and greater than in any of the other endings).
I don't consider the hookup to millions of years of knowledge and each other to be brainwashing though. That's a term that's specific intent, use, and definition IMO does not match what I saw happen - and especially that it was Shepard, specifically, that did it and was the one 'disseminated' to everyone.
Mind manipulation, though? Yes, certainly. I just don't equate that to brainwashing, even when high technology is involved, even when that high technology is suddenly applied to you. We have technology suddenly applied to us all the time, even to our bodies, and even with the at least broad intent to share information and boons. I don't really consider that a brainwashing procedure, though I DO consider everything done previously, by the Reapers, to be forms of brainwashing (one of their biggest faults, and why Shepard is the Good Guy and the Reapers are the Bad Guy), and I DO consider Synthesis to be the most brainwashing-TONED ending, to organics (and Control to be the most brainwashing-TONED ending to the Reapers, though again not actually brainwashing).
That's not to say that it can't be considered wrong. There is a CHANGING of minds. I just do not consider it to exactly fit the conception of brainwashing; that every note of the definition and understanding of that word can be countered by an aspect of Synthesis that says otherwise.
But just as Destroy seems to more ignore having a preserved galaxy and a solution to the greater problem, and as Control seems to more ignore individual freedom and the solution to the greater problem, Synthesis seems to more greatly ignore having a preserved galaxy (that is, 'the galaxy as it was') and individual freedom.
Synthesis is not just the distribution of gigantic amounts of knowledge - it is a form of networking that at least implicitly encourages a sense of One-ness that did not exist before. While the changing of the constitution of organics (or now, 'post-organics') was directly involuntary (but not indirectly, as the 'galaxy's will' was that Shepard find a way to stop the Reapers), it would seem that the connection people have to each other is completely voluntary beyond the initial networked state.
We don't have everyone literally as the Borg. There is no absolute will here. What we do have, is the frequent ability to mentally connect with each other, and the knowledge base to have that connection without flipping the hell out about it all.
It is rather utopian, at least in some ways. And I do have personal theories that it is all essentially fake and The Matrix and a Dream, etc. But still, taken literally, Synthesis, while it personally disturbs and even disgusts me in ways, is an actual posthumanist goal, and not considered by everyone to be as wrong as you yourself may consider it.
There's so much that can go wrong, but Bioware showing us (at least the dream of, heh) Synthesis, is one of the few examples in media where it actually goes 'right', at least in some ways and to some extent.
We've been very used to 'synthetic = evil' and more recently 'synthetic = problematic', that its hard to believe that there can be an integration, to the core, with synthetics in a story without something going quickly catastrophically wrong. And it doesn't help that in Mass Effect, while each game progressively added both optional and mandatory messages that synthetics may not be as absolutely evil and monsturous and they seem from our perception, the Reapers were maintained as our enemy, constantly committed acts that we consider morally repugnant, and their motives and origins largely remain a mystery (even after Leviathan, in a way).
So Synthesis is, in so many ways, a 'leap of faith'. I have my considerations that this has its downsides that the next game may explore (we'll see - again, just personal theory), but I don't think it is as outright evil (even outright evil at all) as people think. I don't think it is brainwashing, I don't think it is impossible (sorta), and I don't think it goes completely against Mass Effect - though I do consider the pacing of it to mess with the flow of the narrative, at least in most character choice paths.