Ah from that perspective I can see how this might appear to be better. Personally, I like the 'magic' of NPM (which to be honest I don't really think is all that magical, it's quite transparent what's happening behind the scenes). This 'magic' means I no longer have to write 200 line makefiles, so it definitely makes my life easier.
Some of that convenience will still be included, a couple of things that deno will do differently from node will be that there is no standard index.* file to load and import path include the extension.
So I basically have to do manually, what NPM/yarn do for me already?