UI's impede development
I develop applications for scientists that consist of two portions, user interface and analysis. The development time for the UI is generally much longer than the time necessary to code the analysis and generally is close to the length of time to R&D the analysis. In addition, the UI is the most fragile part of the program requiring many tweaks to handle odd situations. While UI's can sell a program, they consume a great time of development time relative to the program's core.
UI's impede analysis
UI's limit how programs can be used to only the exposed functions. A person must know THE way of performing a task within the confines of the UI, if one exists. The finer granularity provided by command line allows alternatives. Take for instance randomization of lines in a file. I have no idea how to do this in Windows where practically every program has a UI. However, in Linux, I can immediately think of five ways ($RANDOM in bash, shuf, sort -R, rl, write a small python/C/etc program). The chance of knowing how to perform an operation is greater when there are many available methods.
UI's impede creativity
Composition of small functions, the core of the UNIX philosophy, allows for greater creativity. UI's limit methods to those provided by menus and dialogs. One simply memorizes UI's. The composition of small functions, a solution, is engineered by the person, and does not need to be preconceived by a UI designer.
UI's ensure a churn of future versions
UI's have limited power and generally are not extensible (except, for instance, where macros are allowed). People's needs change over time. These facts combine to result in a stream of incremental changes allowing manufacturers to collect from their clients instead of empowering them. This churn keep the programmers employed but they may no longer be solving meaningful problems.
UI's encourage evolution of software towards bloatware
When comparing software, it's easy to quantify the comparison using feature number. This results in manufacturers fluffing their UI ultimately resulting in a difficult to use UI's, followed by abrupt UI changes during periods reorganization. Reorganization is necessary to slow the evolution towards bloatware.