Choosing a secure element is the toughest part of this project. All the popular ones, (NXP, Infineon, etc) are proprietary & go against the openness of the project & therefore can not be used. In order to keep the openness of the project, I have chosen to base my secure element design off of work done on cryptocores over at http://opencores.org/projects.
The design should be very minimal as to keep the attack surface as small as possible. Also, best practices for side channel & tamper resistance will need to be included.