Some thoughts...
Contains Spoilers...
Let me begin by saying that I liked Berlin Station but just because you like something doesn't mean that it can't be done better. I think the series started with a lot of intrigue and a good premise but sort of ended as a patchwork quilt.
The whole Iosava story arc was over done. If the couple was simply running German brides to ISIL then they made the couple way to powerful. If the eye wash operation was simply to ferret out Thomas Shaw, Hans Richter with the BfV should have been able to provide more clarify information about the couple. That the Iosava's were counter surveilling some of the brides as they prepared to be sent to ISIL seems a bit over the top. Mix in that the wife would receive a phone call a short time after her husband was grabbed, that she would be with a group who was heavily armed and would begin shooting up a shopping mall after the grab. That they would have the technical support staff to arrange the negation with Frost seems a little over the top.
Why was Clay Williams going around having people killed and shredding the whole operation? Better to simply have said it was an eye wash to flush out Thomas Shaw who was embarrassing the whole agency.
I felt they gave the whole Thomas Shaw thing away to quickly. In the end the revelation was Hans was running Thomas Shaw but it would have been more suspenseful to not have the audience know Hector's role and leaving the audience guessing who exactly is Thomas Shaw. It may have been better if Miller was Shaw and was just a way to get back to Germany.
On that thought, the whole Richter and Krug running Thomas Shaw makes no sense. What was the end game of embarrassing the CIA? Was there an exit strategy? They simply wanted to embarrass the CIA station in Berlin and then when their plan might be exposed they simply cower to whomever may reveal their plan? What did he think was going to happen when he started to embarrass the CIA?
I think they made Hecktor a little to caring. Part of working for the CIA is using people. You may be friendly with a person, but they are simply a source of information so that you can get them to betray either someone or something. I get that Hecktor is remorseful for things that he did but the show could have been better in showing the way that they use up an asset and then when the asset is no longer needed or useful they can be easily discarded.
Like I said a good show but there were some ways it could have been done better.