Deciding factors: the large lakefront site offered up by Mayor Emanuel, and, apparently, George Lucas's lingering disappointment with the way the museum's San Francisco proposal had been handled.
Here's the statement released in San Francisco by the museum board:
For over four years, the Museum team has worked and reworked our plans in pursuit of approval from the Presidio Trust to build on the Crissy Field site. When George’s vision for the museum was rejected earlier this year, we began to consider alternate locations outside the Presidio.
The site proposed by Mayor Rahm Emanuel’s task force in Chicago is significantly larger than the locations put forth by the city of San Francisco and the Presidio Trust. Beyond size, the Chicago site has several other important attributes: it is easily accessible via public transportation; it is in the midst of a vibrant museum community and is centrally located in a city renowned for its love of art and architecture.
“Building in Chicago is the right decision for the Museum but the Bay area will always be my home,” said George Lucas. “I grew up here, made all my films here and raised my family in the Bay Area. On behalf of the entire Museum team, I am profoundly grateful for the enthusiasm and support this project received from the Bay Area community.”