You see the Reaper want Shepard because Shepard is the oppest of a Reaper.
Instead of harvesting all life, he/she is trying to save it.
Instead of Indoctrinating the people, Shepard rallys them through acts of heriocs, and speeches.
Instead of thinking highly of him/herself, Shepard thinks about the people around him/her depending on how you play your Shepard.
Shepard stoped the Reapers from arriving with the help of the Normandy, it's crew, his/her friends, and the dead Protheans.
Shepard stoped them from making a Reaper made out of human Genetics.
Shepard stop them again if you downloaded Arrival.
Shepard has made peace with the Synthetics in this cycle, and united the whole galaxy.
The Reapers see Shepard more than a soldier, a Hero, a champion, but a GOD. If the Reapers have Shepard's leadership skills, imagen what would happen if the Reapers have Shepard's admiaration, determination, cunning,willpower. Chaos.
Shepard is the new evolution that the Reapers have to learn about before more awaken in the next cycle. Hence ME4. Maybe new cycle, and if Synthesis happened, then the new harvest starts all over again.