It's different because it is much further removed from a centrally controlled dumpster fire. The JS, Node and NPM ecosystem is a pain on so many levels. Blindly trusting developers to follow semver by default. Leftpad. Build toolchains. The whole micro-depedency madness. Having a peek into your node_modules is like looking into the depths of hell.
Not saying Deno won't devolve into this sad state at some point. Maybe it already has. But it seems to try to combat some of the problems by being honest and pragmatic about dependencies, promoting minimal external tooling and removing some of the dangerous abstractions from NPM.
To me Deno seems like a desperately needed and well thought out reset button.
And this is different from NPM how? Except that I've now lost all the tooling around NPM/Yarn.