The reason is simple, contributing and reading the project source code should not start by learning a programming language. It is a different scenario when a team in a company has decided to learn and write their project with TypeScript/CoffeeScript/etc. language.
About tooling, I think writing modern JavaScript (ES2015, ES2016) is beneficial and therefore, you need a tool like Babel. When you go to that path, why not use TypeScript instead and get ES2015/ES2016 + type system + great compiler?
It may still be a slam dunk to you, but it's not as "obvious" an answer as you make it sound.
What tools are you talking about?
A good example of this is modules. Angular 1 had its own module syntax (partly because modules weren't really a thing when it started). You could write scripts, concat them together and go.
In angular2 we embraced ES6 modules, which means a developer has to deal with loading and bundling etc.
One nice side effect here though is we can leverage more tooling from the rest of the JS community (eg, the great work of webpack) rather than having angular-specific solutions.