I work on this project.
One crucial thing to make the GUI simpler than code is direct manipulation. Working with a graphics program, like Inkscape, for example, is much easier for most graphics tasks than writing raw SVGs.
For most tasks in Lyra, you can simply drag-and-drop elements onto the visualization to make it respond the way you want. In advanced cases, true, you do have to navigate menus and buttons. For many of those cases, rather than writing raw D3 code, there's the Vega project. Vega is a declarative format for describing visualizations using a JSON format. Lyra generates Vega specifications for rendering, which can then be modified manually.