Was Shinnie changed that much in connection with its hosting duties?
This is almost a rhetorical question with respect to US Open venues, as the answer could be all of them. From recent history the USGA seems to have left its mark everywhere, including courses that have been open for less than 10 years and have yet to host their first Open (EH and CB).
ANGC probably wins the award for most total changes. Hosting an annual event and being on the progressive side of adjusting the course to fit the modern game are two of the reasons why.
As for the changes with the greatest impact, the preparations taken at Bethpage have done wonders to revive the glory of the complex. There's a similar discussion to be had regarding what we'll be seeing at Pinehurst.
As for the course that least resembles what was once there, Congressional probably wins.