The essential premise is that the Collectors are kidnapping humans to study them for Indoctrination. The brain is complex. The nervous system is complex. And important differences exist for each species. To manipulate those very complex biological systems, the Reapers require a great deal of study and testing. They require a great deal of understanding for Indoctrination to be effective. Shepard arrives at the base and finds thousands of asari, salarians, turians, etc., dead but preserved for millenia. The Reapers have to study their biology to make Indoctrination work, and having been doing so for a great deal of time.
The indoctrination we saw in ME 1 was not 'true' Indoctrination. It wasn't effective. Both Saren and Benezia, the only two people subjected to long-term 'Indoctrination,' were ultimately able to resist. Sovereign was able to kinda-sorta Indoctrinate people in the same way a person who has no understanding of a machine will likely kinda-sorta be able to get it working merely by messing around with it long enough. But ultimately, it led to unstable psychotics instead of reliable and effective servents. The Reapers need 'true' Indoctrination for their conquest. (Ideally, of course, this would involve some backtracking to ME 1 to alter the portrayal of indoctrinated characters somewhat, but it's not indispensible.)
The reason why humans are being abucted is simple. Previously, they were beneath effort. New to the galactic community. Only 30 years on the playing field, and so the collectors didn't bother. This changes with the events of ME 1, where Sovereign is stopped by a human and human fleet, causing the Reapers to re-evaluate humans and conclude the danger of a powerful species above indoctrination is a larger concern than whatever attention the Collectors will inevitably bring on themselves from a sloppy harvest hastily conducted in a few months instead of the hundreds or thousands of years they usually permit themselves to slowly gather subjects from remote corners.
So, long story short, Shepard destroys whatever data they've gathered somehow, data on humans and aliens alike, cutting off the ability of the Reapers to effectively indoctrinate. This has a great deal of advantages.
- ME 2 is no longer 'pointless,' as people whine. The Reapers are struck a very significant blow, yet still remain incredible powerful enemies for ME 3.
- Indoctrination is no longer a concern in ME 3, which addresses some issues and makes the allied resistence more plausible.
- No Reapers made from goo rubbish, no human Reaper.
- Removes irritating 'humans are special' themes. Humans are no longer biologically special at all, just the last in line.
The choice is also improved. Shepard now has a much stronger reason to destroy the data instead of giving a copy to Cerberus. The data is not some vague collector technology, but technology specifically and purposefully designed to subjegate a thinking being. It's technology designed to enslave. Paragon players have more more justification in reasoning that such technology is an abomination and that Cerberus should absolutely not get their hands on it.