hmm, so many places.
Pyramids at Meroë: An ancient Nubian site, it's been looted, plundered, and bombed over the past 1600 years. Because of the uneasy political climate in Sudan, it hasn't been properly excavated in years. There hasn't been any major studies of the area since the 1920's (or 1947, if you played the Infernal Machine)
The Yucatan: Now a major resort and vacation area, but there are still vast stretches of the jungle that haven't been mapped. Most likely, there are Mayan cities and structures that have been swallowed up by the jungle vegetation. Recently, with the help of satellites, some of these undocumented places have been found. The same goes for much of Mexico and South America, there are still countless Meso-American sites that are waiting to be found.
there's also the Ziggurats in Mesopotamia, although they've been looted and excavated, it'd still be great to explore... despite the insurgents.