I like Pluto as well, but the project baked in opinionated choices which imo make sense for hosting course notebooks for a class but at the same time make it annoying to use as a tool.
Besides the often commented upon cell outputs that appear above the code and the forced begin/end blocks, Id rather see better control mechanisms for pausing/replaying execution, to have the notebooks play nicely with the existing package environment system instead of being self-contained, and to function outside the browser (eg with VS Code support).