The defensive systems are the same I'm sure, it's just certain "bugs", I suppose you could call them, occur when you switch to a player in your defensive line. For example full backs tucking in too much leaving their wing exposed, or center backs being susceptible to lobbed through balls, or DMs tracking runners too far butchering your defensive line. I found that you can mitigate these situations by being cautious about player switching, or controlling a center back and making him drop deeper while using second press to pressure the ball carrier (this negates aerial through balls).
Either way, defending as a human player is immensely satisfying in PES, I had some great matches on the demo where I was one up in the last ten minutes and went ultra defensive and had to defend backs to the wall with wave after wave of CPU attack, the way you defend in those situations almost perfectly replicates Chelsea against Barcelona/Bayern with your team huddled around the edge of the 18 yard box.
Yes there are flaws but overall the AI in PES is streets ahead of FIFA, but as I said is severely hampered in other areas.