I think the biggest miss was not making mixed mode (default) for Node do it the way webpack/babel, etc did it by default in terms of interop. I get they wanted to make it more implicit to call cjs from esm, in the end it just inhibits conversion of existing libraries as dependencies are now a bigger hurdle.
Frankly, I like the Deno way of things better. I find it annoying, to say the least that the TypeScript team won't consider allowing you to import with a .ts(x) extension, and convert to .js(x) as part of the build process... no, you must omit the extension.
I've been using the import/export syntax since well before it was standardized via babeljs, these days I kind of want to remove webpack/babel from my pipelines altogether and mostly just rely on esbuild. I've also been using/following rome.tools development, having switched over several projects from eslint already, and will probably start with their bundler when it's ready.
I think there's a way to go with tree shaking and static analysis in that direction to reduce load. I also would not mind seeing the efforts to treat TS extensions as comments in the JS engines in that it would be easier to serve up straight TS/JS without bundling/minifying. I'm not sure we'll ever see a return to that in practical terms.
In the end, it's evolving. I'd also like to see Cloudflare, Deno and others come together on a more common server interface so that you can target multiple clouds with a single codebase. I don't know how well that would ever work out at this point though. There's aspects that I definitely like to all of them.