To be 'fair', if we're to take the direct and literal presentation of the plot:
1)Synthesis was not what the Reapers were looking for. What they wanted was the Cycle. What specifically Harbinger wanted was humanity harvested in the Cycle, and he seemed to possibly be the most experimental about it is all.
2)Synthesis was possibly not what the Catalyst/Intelligence was looking for. It had tried a 'similar solution' but perhaps not actually it. It was also perhaps not looking for this solution anymore, but you showed that it was possible.
3)The Reapers do not seem to be actually looking for solution. There may be some curiosity about some aspects of finding it, but they also seem to be set in their ways as the Cycle being the best they can do, and the best that can be done. Picking Synthesis goes against this position of theirs, and even the Catalyst communicates that it was never expecting such a thing to happen. What I mean is that its agency by Shepard, not the Reapers.
4)What Saren boasted with man and machine intertwined is not necessarily what the Reapers intended for him, but simply the conclusions he came to through interface with the Reapers (as in, its their ideal, but not necessarily their PLAN). Saren was looking for a way that organics could survive in some form that leans at all organic. It was a flawed and dangerous and cowardly approach, primarily because it accepts loss and accepts subservience and we see what the Reapers think of 'man and machine intertwined means' so far (Collectors at best?), but the principle that he was hanging onto wasn't necessarily what all indoctrinated individuals believe. We see many more examples of what the indoctrinated can come to conclusions about, and it may depend on what 'organicness' is left in them. Some despair more, some worship more, and some bargain more, etc.
Basically, Synthesis might be considered not a surrender, but a last-minute peace talks between organics represented by Shepard to end the war (the script is very particular about ending the war and stopping the Reapers being the big thing, and destroying them just being the most definite and clear way to do so, with anything else being a gamble or distraction from destroying them), and end the synth/organic conflict if he has interest in it (there is dialogue throughout the game that brings it up as at least an issue), and the Catalyst that wants to end the war and cycles if it solves its problem. That is, we're not slaves but at the right moment, we may be at least much closer to equals. This is arguable though, since it appears the description and results may favor 'Reaperness' rather than 'organicness', ultimately. But its not a direct surrender, is what I mean. Its not directly Saren.
All this is to say that Synthesis MAY not NECESSARILY be a surrender (who is losing and how? is this really a war or was it a larger process beyond even the Reapers' plans?) and MAY not NECESSARILY be giving the enemy what it wants (the Reapers themselves still wanted to Reap until Synthesis, and the Reapers didn't seem to intend on the exact consequences of Synthesis at all). It could be more described as reaching peace and giving both sides what they need - though you/Shepard and the Catalyst being the judges of that is arguably a final step (way?) too far in deciding things for the galaxy.
To make perfectly clear, Synthesis, to me, IS a surrender and IS giving the enemy what it wants. I was just considering some greyness to this thinking and some devil's advocate.
EDIT: I also get creeped out whenever I think of all the things I listed above being pretty much false because its all just a grand manipulation of some sort to get Shepard into the decision chamber, real or virtual or whatever it is, to ideally-to-them 'freely' pick Synthesis and cause something at least mostly terrible. That Synthesis is 'best' in ME3 but may be seen to be 'worst' or one of the worst, or at least more complicated, later on in the series, assuming IT or anything like it ends up remotely true on this matter.
EDIT: One plus I can imagine is that a Shepard picking Synthesis is clearly one that is now making a statement by actions to pursue what it considered to be peace and progression and even transcendence no matter what. For all its complications or even horrific possibilities (even in literal story, we at least in the short term have what seems to be sapient/sentient husks connected with all now neo-organics LOL), what it could say of Shepard is that they desire to be what they consider to be pure of heart and intent while surrounded by pain, death, and corruption, and that certainly is something newer to ME3's RPing and its own special strain of dialogue and actions you can take. It could be meaningful in any sort of continuation of plot - if we disregard all of Bioware's indications that we're not dealing with Shepard again.
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