little late into the thread to answer, but o well. this one is easy.
of the options that, as i understand it, have not become available in PES3, here are just a couple that i would implement:
visible referees/linesmen?fourth official(also, when the time is announced/substitution, thing should be raised)
animated managers on touch line(we've all seen martin o'neill when the odds are stacked against him)
the ability to run away from referees(not really, i just remember that from one of my first footie games, the first FIFA back in the day. you could run away from the ref and not get booked. good times.)
naming the starting line-up when the players come out during the intro scene
first names for players when being announced but shortened if they score, ie Henrik Larsson is up front/o! and Larsson scores a wonderful goal
stats:"that's his fifth goal of the season!!" and more stats coming up when they score, not just height, name and age. # goals in game/season would be good.
that would be about it, other than updated squad lists(or as the yanks call em, rosters)
A BEEZE!