Q:

What differences are there between Prime Directive d20 and Prime Directive d20 Modern? 

There are 2 versions of Prime Directive d20, one based on the D&D 3.5 PHB and the other based on D20 Modern.  Are there any noteworthy differences between the two versions, or did they just make a second version of it for people who had d20 Modern but not D&D? 

A:

I asked on the Star Fleet Universe Discussion Boards, and received the following answers:
Answer 1:

The two rules sets are somewhat different and while a good GM can make
  either one work with the other (after a fashion) d20v3.5 and d20M are
  effectively different game systems. 

Answer 2:

The two rule books (like all the Prime Driective rulebooks) share 60
  or so percent of material.  This being background, fluff, fiction, etc. 
The rest of each book is system specific and there are enough
  differences between D20 and D20 Modern to require two separate books.  
While both systems work for PD, I much prefer the D20M version.   In
  D20M, your character classes are Strong, tough, Fast, Smart, etc. 
  rather than Warrior, Mage, Priest, and Rogue. 
The skills and feats avialable are more in line with a futuristic
  setting as well. 

You can follow up if you have more questions at the Star Fleet Universe Discussion Boards.