Researchers are paid to churn out papers, working under publication pressure. As you can imagine, the result is not the best, most user-friendly software.

(Making software is difficult. Adding publication pressure is not going to help the process.)

So, there is a second class of people, called scientific programmers, who might do what you imagined. However, their work is undervalued. For example, although they are often listed as authors of scientific papers, they will almost never be first author. And this type of people will also be the first to disappear if funding dries up. Further, when writing scientific proposals, nobody thinks about hiring a scientific programmer, or it comes as an afterthought.