Well, in general the problem with flash was the plugin wasn't well isolated, and often would crash the browser, and before NT-based windows was common the entire OS pretty readily (presumes windows). Not to mention the security track record. Browser isolation, and how well it will likely be with wasm is quite a bit different.

That said, it will lead to more closed commercial sites, but the JS outputted from webpack+babel+uglify is already unbelievably difficult to wade through without source maps. It's not significantly different imho.