I completely agree. While asm.js has its problems, its moving in the right direction. Honestly, it seems like this wouldn't be too hard to add a backend target for asm.js, if its implemented well.
Note that asm.js (and probably PNaCL as well) currently offers very little for languages like Scala that need good GC. Until that's addressed simply targeting JavaScript is going to be best approach for these languages.
I don't think running a garbage collected languages on asm.js will ever make any sense (since it would mean implementing and shipping your own GC as part of the application source). So, yeah, you're right. Scala (as-is) is not a good language to target any of the "native" targets like asm.js.
