Sorry Forest Athey - on topic, Indoctrination is the way Reapers subdue targets in prep for use; be it via control or to simply harvest them for biological resources. Shepard could be useful as a puppet, or simply used as raw genetic resources if they could find a way to harness will, determination and spirit. I'm also not sure it's about the final run specifically, but more about the process. Shepard is constantly tested and always seems to prevails, but the cost weighs on them; wearing them down. Shepard is also referred to as an anomaly by Leviathan, though it's never clear what they means.
From the perspective of the final run, you could say control of Shepard was the goal, and manipulating Shepard into not destroying the reapers was the end game, but there is way to much to chance unless they know something Shepard doesn't. To your point, I agree. It makes no sense to indoctrinate Shepard - at least not for use as a puppet. As for Saren, his indoctrination makes more sense, but Eden Prime does not, unless The Reapers needed the Beacon for something other than finding some mystery conduit. Pre-exposure, Saren could have just walked right up and activated the console in the Citadel tower, gave some flase evacuation order and prepared to closed the arms once Sovereign was inside without anyone questioning him - and there wouldn't have been a fleet blocking Sovereigns path into the Citadel - not that a fleet mattered. The harvest would have been over before most of the galaxy knew what was happening.
_
Off topic one last time to respond to Marolf - I never said anything about time travel. The entire trilogy takes place in Shepard's head as their body rests comfortably in stasis (some time after the EP beacon explosion) and their mind experiences the 'warning' in the form of a history lesson on the Reapers, all while fighting off indoctrination. Even the ME1 box art hints at a matrix like virtual reality.