They kinda did that though, didn't they? The Collector Ship at the beginning of ME2 targeted the Normandy specifically and basically killed Shep, but they probably hadn't expected Shep coming back to life.
Also Arrival DLC? They indoctrinated Kenson to lure Shepard into the trap and get rid of him/her in that way.
I am with StealthGamer92 on this, I think Shep made humans interesting enough for them to further study them.
I try not to think too much about Arrival, because if they were trying to get rid of Shepard, they could have easily done so once Shepard was taken down, which is unavoidable.





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