One thing I struggle with is, like jka says, to communicate trade-offs and to gather requirements. In other words, solving the underlying problem; not the symptom without causing bigger problems in the future.

The main thing I miss is to be able to, as Fred Brooks says, "throw one away". It happens too often that, contrary to the second part of Brooks saying (i.e., that "you will anyhow"), something that should be a prototype ends up as the "finished" product, causing headaches down the road due to shortcuts that were made or because whatever was learned in developing the prototype is not taken into account due to time pressure. On the other hand, I work in a small company and the customers are happy enough, just too few so it might be the case that these headaches are a reasonable price to pay.