Take a look at this MSDN thread:
http://social.msdn.microsoft.com/Forums/en-US/ssdt/thread/3110809b-fa51-485e-91cb-4f530f84c924
There are no global settings, but you can save a comparison as an .scmp file, which includes your comparison options. Also, if you create a Schema Compare file from the SQL menu (so it has no selected source or target), set the options you want and then save the file, you can create a template for future comparisons.