Problems

St. Pauli has problems with the structure against the ball, and it has been hurting them a lot this season.
St Pauli does have problems. It is not just that they have a lot of injuries, which has really affected their performance, but it is also beyond the personnel. It looks like they have problems against the ball (out-of-possession).
St Pauli have lost four of their last five Bundesliga games. The fact that they came up against the likes of Bayern Munich and Bayer Leverkusen, who have better quality, may help to put some of those defeats into context. However, the defeats in those two games weren't that big (the difference in goal difference was only one in each case). And for the game against Leverkusen, one of the reasons for the defeat was related to the problem that this article wants to talk about.
After the first three games, in which they played with front-foot against the ball and pressed hard, St. Pauli dropped their intensity. Coach Alexander Blessin has realised that it is too risky for the team to play aggressively out-of-possession, as they are exposed to a lot of transition attacks. St. Pauli defended deeper, waiting patiently for their opponents to come forward and closing down the middle of the park as they didn't want their opponents to get the ball through.
In this way, St. Pauli has a 5-2-3 structure on the ball. The front three usually form a narrow position (again, to close the central area and the passing line to the opposition's central/holding midfielder). Behind them, two central midfielders also formed a narrow position, often attempting to man-mark the opposition central midfielder. The five players up front thus created a kind of box-pressing to shut down the opposition's central area. With the centre closed, St. Pauli seemed to want to trap their opponents in the wide areas, making it easier for them to lose the ball.
But by forming this narrow block, it also creates space in the other part of the field. The half-space is a bigger concern than the wide area. It's often exploited by opponents. With five players upfront close to each other, it makes the defensive line vulnerable. There's a gap in front of them sometimes, and they also need to face opponent players not in a numerical superiority situation. St. Pauli often conceded from these situations.
I first noticed this in the game against Borussia Dortmund. Dortmund often put their players in the half-space to create superiority (2 vs 1) against St. Pauli wing-back (who didn't have protection from the central midfielders or attacking players) as the full-back of Dortmund also moved forward. The first Dortmund goal came from this problem.
And then St. Pauli kept conceding because of the same issue. The second Borussia Mönchengladbach goal, Leverkusen's first goal and Werder Bremen's first goal from last weekend's game are good examples of this. In the game against Leverkusen, St. Pauli really struggled if the opposition was able to exploit the half-space and the space between the lines, especially if the players in that area were strong (like Florian Wirtz in that game).
Bremen coach Ole Werner also exploited this problem. At the Millerntor last Saturday, Werner realised that by moving one of his attacking midfielders (Romano Schmid) closer to the centre, his team would have a numerical advantage in the middle and put the Pauli defenders in a dilemma (to press or not to press). This makes it impossible for the St. Pauli central midfielders to man-mark because they are in a 2v3 situation. The St. Pauli defenders can jump to help, but this created space for the Bremen attackers to run to (also one of the situations Bremen were hoping for).
With a numerical advantage and the St. Pauli defenders in a dilemma, Bremen were able to score. Bremen took full advantage of St. Pauli's situation, especially in the first half. Blessin later realised this and changed the structure to 4-3-3, as there were three players who had to man-mark three Bremen midfielders. This structure helped and also has its problems, but that is another story.
Another thing that needs to be emphasised about the 5-2-3 structure is that St. Pauli play is the dynamism. St Pauli looks too passive. Their first line (three attackers) is very easy to pass through, and when the ball is already in the second phase, sometimes there's no follow-up situation: To overload certain areas, to press certain players. It seems as if they are just waiting, and this leaves their defensive line easily exposed. Their lack of intensity in certain moments really hurts them.
Well, it is not about they need to press as much as they used to, but how the team can know where and when to press more, when to go for duels, when to win the ball quicker. I asked Jackson Irvine about this after the Bremen game and he said: "Overall, you can press as well as you want, but then you need to win the duels, and try to take the second balls. We did it okay, but with the intensity and the aggression we want to play is not nearly well enough.”
There's something missing, and the passivity of the 5-2-3 structure that St. Pauli have been playing looks like it needs to be fixed. There was a moment in the game against Bayern when St. Pauli defended more with a 5-4-1 structure, with the wingers dropping back and covering the half-space. It helped to keep Bayern from creating many chances. Blessin could try this idea again. Yes, it is more passive in the first phase, but it can help St. Pauli to overload certain areas and cover the back line more safely.
Or, if Blessin wants to push forward more (as he says in Tim's question), he can use the 4-3-3 structure he used in the second half of the Bremen game by moving Eric Smith into midfield. The only thing they have to do is to be more careful with your defensive line (to be able to move from one side to the other), so that it does not get disorganised and create spaces. This can also be done if your opponents play a back-4 formation.
In short, that needs to be fixed. And St. Pauli really needs the winter break. It is not just to wait for a few key players to return from injury or for new signings to arrive. It is also about giving Blessin and his coaching staff time to sort out these problems. Because St Pauli really has the chance to go from not good enough to good enough in many phases of their game.