Wasn't this Saren's ultimate goal?
To be exact, Saren's goal shifted as he changed his mind/was Indoctrinated more/Sovereign's plan advanced.
In order:
1)Find a way to stop, fight, resist the Reapers, and go along with Sovereign for now. (I think this was his plan at first?)
2)Go along with Sovereign as an ally, to let the Reapers in, but put chips in various research (and maybe other connections, but that's just theory) in order to find a way to at least counter the Reapers, or at least the Indoctrination occurring.
3)Reapers appear irrefutable. So Saren submits to Sovereign, still considering himself an ally. He believes by this point that the Reapers can only improve organics, but only if organics submit to the Reapers. On the Reaper's terms.
4)The Reapers must arrive. Saren openly submits to Sovereign, as a servant. He claims that Sovereign is impressed by Shepard, and that the merging of synthetics and organics is the future, and that we'll be reborn through joining Sovereign.
So what's the difference? Well, as presented by the ME3 ending:
-The Reapers' Catalyst presents the choice, but we can pick anything else. We always have other choices clearly available to us.
-Merging between organics and synthetics are done at a level that we've never seen the Reapers capable of before
-As far as it appears, Synthesis is not on the Reapers' terms and power, but ours. And it ends up seemingly putting everyone on a generally equal power level, instead of submission to the Reapers.
Saren was trying to set up a situation where organics were 'spared', but only to be implanted/changed/experimented/etc by the Reapers as they see fit, and the Collectors are introduced in ME2 as a consequence of that. So even if we are very trans/posthumanist with our scifi sensibilities, we have to know that submission to the Reapers is just not a heroic thing.
But apparently building a giant weapon that can be turned into a tool that can seemingly override any Reaper control and make the Reapers feel connected to organics at an innate level, including encouraging 'humanity' in them? Hmmm.
That doesn't sound like the same thing as "Yeah we have to do what the Reapers say about everything because they're gonna kill us all otherwise dawg." In the Decision Chamber, we don't even face that latter part. We always have Control and/or Destroy available, and they have to do more with a larger 'synthetic/organic problem solution' (as explained by Catalyst) than 'you'll all die if you don't do exactly as we want'.
But I'll admit that Synthesis is closest to what Saren wanted by the end of his Indoctrination journey, and it does carry the most related risks. For all we know, we did Reaperfy everyone in Synthesis, and that can be considered a total Lose ending, in that sense. Even if that Reaperfied form looks very different than all especially ME1-ME2 examples, and we were presented with a clear choice instead of convinced that there was only one choice.
There may even be a difference made between the 'Catalyst/Intelligence' and 'The Reapers'. The Reapers would appear to still want the Cycle To Continue. They may or may not be actually aware of the Catalyst themselves. So if anything, they may only 'want' Refuse. But the Catalyst is the Collective Intelligence, being made of and calculating the intelligence of all of the Reapers, and that combined with being in the Citadel while combining with the Crucible = deciding that Synthesis (if available) is the way to go.
So what are we submitting to, in that case? Before this stuff of ME3 ending, 'submitting' was only understood as:
1)Just waiting to die, instead of DOING something
2)Turning right into Reaper tech without alternatives/differences, considering it the only way of evolution, without care for being controlled by it
The Crucible technology would appear at least to go against this.
1)Using it DOES something AGAINST the Reapers
2)It INVOLVES Reaper tech, but acts as separate technology, in accordance to resistance against the Reapers
Control and Synthesis may be really skirting the line between helping/hurting the Reapers, but that's why we have those Paragon replies since ME2 (maybe ME1), where Shepard says they'll 'stop' the Reapers, not 'kill/destroy' them. A Paragon may aspire to achieve great success at the supposed impossible, and both a Paragon and Renegade may take a turn towards attempting a miracle (even a Renegade could pick Synthesis easily because it 'kills' the Reapers into something else, just as they may see it as 'killing' organics to make them something else).
Anyway, my main point is that Saren positioned himself as a slave, while Shepard seemingly positioned himself as ALWAYS the opponent, or even superior to the Reapers (at least in the moment of the final choice).
Could he be tricked about this and wrong and Indoctrinated and blah blah? Okay, maybe, yeah. But it would still have been through the framing that Shepard was FIGHTING the Reapers (even in Synthesis, even if its at more of the ideological level), not actively working FOR them. Even if Indoctrination Theory is real, imo, for example --- I like to think that even Synthesis would produce something that would reflect that Shepard kept enough of himself alive, continuing, someplace/where/who. Because even Synthesis was not submission. Merging isn't submission. But it is assimilation, so I still have concerns
.