+1 to driver and Merdeka Square + perhaps one shopping mall depending on your interests. Batavia Cafe is a classic.

Another option would be to see about getting a day room at the Mercure Batavia. It's very close to Batavia Cafe/Merdeka and relatively close to the airport.

Yet another option would be to get a day room at one of the hotels near to one of the airport train stations, nearly all of which are also near shopping malls. Take the train in, freshen up, take a cab to Batavia, have a bite at Batavia cafe and maybe visit one or two of the museums in that area, then back to hotel/shopping, then train back to airport.
The train doesn't run all that frequently but it isn't subject to the same traffic concerns.