This is, arguably, the largest non-gameplay change between 1.1 and GPP.
Frags/Kills are just basically the the number of aliens/humans have you fired the last shot upon, regardless of total percentage of damage.
Score offers a points based on damage done (meaning you get points from assists) and base destruction.
While I find score to be superior to frags on the grounds that it is a more holistic representation of your overall performance, it is far from perfect. I'm curious to hear what other people's take on this is and whether other people care to see how many kills they have (I personally am against this. I feel it promotes camping for a high killcount against weaker opponents instead trying to win the game). Also, feel free to propose alternative forumla for score calculation.