For a Mac, if you go to your hard drive, then on the places tab, click your username (the name next to the little house icon), then into library/application support/adobe/illustrator/new document profiles. You should be presented with 6 profiles (in .ai format).
These 6 profiles are your defaults, which you are prompted to use every time you start a new project. You need to open the profile which you use most commonly (or all 6 if you wish).
Once you've opened the document, ensure that you've got the 'graphic styles' window up, then draw a line with the desired stroke and colour. Then drag and drop this line, using the selection tool (black arrow), into the graphic styles window, onto the little box which says 'default graphic style'. This will then create another box. Then save the document.
Now, when you start a new project, select the profile you have edited in the 'new document profile' drop down list, and inside the graphic styles window, your newly created stroke and colour should be selectable. Unfortunately this doesn't entirely solve your issue , but it does mean that you now only have to click one button instead of 3047. I hope this isn't too confusing.
Let me know if you do find the complete solution, as I'd be interested to find out how it's done properly.