Here is esentially what I do (albeit briefly):
Usually I'll score goals on through balls when I counter-attack afdter being pressured in my end. Usually that means I steal the ball with a midfielder, pass up the middle to one of the strikers (4-4-2) and occasionally as I'm taking that pass with the striker moving back toward my own end I can whirl and drive an lobbed through ball to the second striker. I use the lobbed through ball alot just generally.
What happens in 06 is that anytime the ball is moved up to the strikers or near, the other stiker(s) runat the guy with the ball and then by him. If you take the ball and hold it up, you can also sometimes hit the cutting striker just after he clears you and is running diagonally still.
In FIFA 05, there were a lot of easy through balls where you were angled to the recipient and just fed the ball through the gap. The AI is better in this respect in 06 so its very hard to do that unless theres a huge gap or you're already ahead of the closest defender.
Most regular through balls that I feed that wind up in the back of the next usually are thrown behind a defender and the other teammate runs onto it, whereas in 05, it was usually fed in front of the defender as you led your teammate into the gap with the throughball.
Most times, unless I'm trying the quick counter-attack, I really work the ball around just with the normal passing. If I get down near the end line and am too crowded, there is usually a trailer at the top corner of the penalty area that I'll feed it back to. I just keep moving back and forth feeding it in and out until I break the defence down or I have some space for a long shot (unobstructed by a defender). Unlike 05, don't be afraid to shoot from outside the penalty area, I've scored a lot of goals from just outside. The defenders always try to block the shot and frequently it riccochets of them into the net or riccochets to another one of my players who'll finsih on the ground or in the air.
Cheers,
Dave