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This might actually be a great direction to go.

I don't think there's any particular reason that WASM has to be more obfuscated than JS. You can already throw a WASM file into a bytecode-to-text translator which is about as useful as deobfuscating a minified JS file, and I assume decompiling/debugging tools will only get better in the future.

For a long time now, I've been thinking of a future where your OS properly isolates all the programs that run on it and even gives us the ability to have direct control over how programs interact with the rest of the system. OS's seem too mired in backwards-compatibility requirements to make big changes like that any time soon, but that's basically the way our browsers already work. Download some code, and execute it (relatively) safely because it's sandboxed from the rest of the system. Our browsers are basically the new OS, and this time around we can do it right using what we learned from OS's (and hopefully backport these browser features into the next generation of OS's).

For example, an app asks for a filesystem handle. You can hand it one that refers to a real location on your OS fs, or you can hand it a completely virtual fs that won't affect anything else on the system.

Whenever an app asks for a resource, being able to hand it a virtual or sandboxed one instead is a huge gain for user-control.