Here it is. Someone must manually deploy the landing gear. That's the lever or linkage I remembered. The linked article also discusses other aspects of "autonomous flight" (as compared to remote flight) and while some of the testimony is confident that it could be done, others mention major software and hardware changes.
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http://commdocs.house.gov/committees/science/hsy86869.000/hsy86869_0.htm
Q3b. What technical barriers, if any, need to be addressed to develop a fully autonomous Shuttle?
A3b. There are no technical barriers to such a development. The only significant modification necessary is to automate the landing gear deployment process, which today is manually controlled by the Shuttle pilot.
Autonomous vs. remote-controlled is indeed a huge difference. Autoland is "autonomous," and (aside from the landing gear) is already there. I cannot imagine that it would take major S/W or H/W changes to change this to a ground commanded operation (it's the sort of stuff that's been done on satellites for decades). An autonomous release of the gear is likewise not that big a deal.
What you wouldn't want is to have a piloted landing with autonomous gear-down: that's asking for trouble.