pdflatex doesn't really help here. pdflatex allows you to bypass dvi, the native TeX output format. The input for latex may well still include eps image files though.
True. Of course you can still use EPS, you just have to find another program to view them in. And isn’t there a tool in most TeX pakages that can convert it to PDF, then you should be able to use that at as an input if it makes it easier?
I used to use PDF because you could easily export them from Illustrator and suck them straight in to xelatex or pdflatex (but this was years ago, so I can’t remember all the specifics)