Actually recent versions of Illustrator can create Level 2 EPS. As can be seen from the screenshot below, Illustrator 17 by default writes Level 2 EPS (I have also selected "Illustrator 3 EPS" for better compatibility with Mathematica's importer):
I have successfully imported EPS generated this way into Mathematica. But in general it is better to save as PDF for this purpose.
Also you can use Poppler for converting Level 3 files to Level 2 as I show in thisthis answer.
