Again, this isn't based on this season as that's settled. only a fool would argue that Puyol has been better than Samuel. But in the past 4 seasons Puyol has been playing some of his best football as a defender, carrying barca's defense on his shoulders in the two notable seasons of 2005 and 2006 while their first CL this decade was also due to some heroic displays from him. While Samuel was struggling with an inter team that could only dream of 3rd spot after each disappointing season. Even after those two seasons, Puyol was a rock solid with his NT winning the Euro 08 with good performances when Samuel was struggling in Europe this time.
Prior to the last couple of years, I was only watching Puyol in the CL, so I have a limited view of how he did.
I consider Samuel a better defender than Puyol, but I consider Puyol the better footballer.
Overall, I would say they, at the best, are of a similar level.
I don't agree about defenders in high defensive lines. In fact few defenders can play in an extremely high defensive line in an attacking team like Barca and still maintain their status as one of the best defenders in Europe. Puyol and Pique are often left to defend individually against strikers with there being a lot of space for the striker to take advantage of.
I don't think Barca CBs are left exposed all that often.
The team's ability to maintain possession, coupled with the brilliant pressing of the ball Barca do as a team mean that I don't think they have it all that tough.
There is space in behind, but Valdes is pretty good at acting sweeper, so there isn't actually a huge amount of space to expose in most cases.
In a deep defensive line like the one Inter adopt, There is little space between the keeper and the centerbacks, that more than often works in the defenders favor. Samuel struggled when forced to play a high defensive line with Real Madrid.
I didn't see much of Samuel at Real, so I can't really comment on that.
What I will say is that I'm sure that Real Madrid team did not work as hard or as well as this Barca team when it comes to pressing the ball and protecting the CBs.