I play counter-attacking football in PES3 myself, and it's my best strength.
I use a 3-4-3 formation, but the key to the success of counter-attacks are the three strikers. A target man who has good technique, decent passing, and is fairly good in the air, and the two wide strikers (in WF positions) should be pretty quick, good at dribbling, and have good awareness-type attributes.
Often, when you intercept, they will hover wide around half-way, and they're not normally picked up the defenders. You've then got two options: hit it over the top for a Thierry Henry-type player to chase, or (if a viable option) thread it through for them to latch on to,
or, alternatively, you play up to your main central striker, either in the air, or on the ground, who then releases to either wing, with a nice little 'round the corner' pass, with his back to goal. Works for me.
