It's important to remember that while, yes, CommonJS made Node popular, it did so because it filled a void in the Javascript syntax and specs. There was nothing to formalize the concept of a "package" back then.
That's not true any more, ES Modules have made it into the spec, so that's what Deno is using.
As for package-lists, the current convention in the community at the moment if you have a decently sized library is to have a `deps.ts` file where you re-export all of your dependency, making it an equivalent to package.json and helps with upgrading dependencies across a codebase.
TypeScript is already optional in Deno! it will run any .js file just fine, and you even skip the compilation part.