ISS and PES are two different games.... sure it started off as ISS and then became ISS: Pro Evolution Soccer, but they branched it into two different games. You might remember for a while PES was released on the PS2 while ISS was released on the cube, xbox and gamecube. They were made by two different development teams. They eventually stopped making ISS to concentrate on just PES.
http://www.gamefaqs.com/console/ps2/home/589588.html <-- ISS 3 on the ps2
As for the question. PES all the way. FIFA is horribly dull.
Both made by Konami and yes, after ISS: Pro Evolution soccer you can excuse our 'mistake' the ISS series is not around anymore but ProEvo is released yearly. To me and my bro ISS is just the name of a series of games which held the ISS tag, Pro Evo did once.