There are lots of things you can do to improve your tools. Often, they are found just by treating your tools like products. This means not treating them like throwaway scripts and not just hacking on them as needed. Instead, they need to be invested in, loved, and maintained.
One way this often comes out is by having what is referred to as opinionated tools. This means tools that do not support every single possible workflow. Instead, they focus on the right and wrong way to do things. The downside of this is that tools can be unable to support new workflows when they grow within the organization. As an upside, though, you as the maintainer know exactly what workflows exist and how they work, and can research improving them to make the experience better.
That does not mean that tools should not be configurable. I, personally, love configuring tools through configuration files and environment variables. Configuration files are great when you need to keep all of your configuration...