As far as NaCl goes, the absolute last thing the web needs is portability/endianness issues. I'm writing this comment on a phone (ARM), and I also browse on my desktop machine (x86-64) and my netbook (Atom, x86). (Not to even mention PS3/XBox 360/Wii/older Macs, all of which come with browsers.) Wanna make web the web worse? Force developers to target several architectures for their apps, or greet users with "Your CPU isn't supported!" pages. Lots of Webapp developers have trouble with cross-browser issues!
If you look at Firefox plugins (native) versus extensions (Javascript), you can see fairly plainly that, even though it's slower, the ease of development in Javascript (even with all its quirks) outweighs the benefits of native code, even for heavyweight extensions.
The best solution, in my opinion, is to expose a (fast) bytecode VM to web developers. Javascript is okay for a lot of purposes, but it's a messy language, and can be pretty clunky. A bytecode VM (one that at least has a Javascript front-end) could solve most of these problems. Off the top of my head, the JVM has Rhino for JS (as well as support for Ruby, Python, Clojure, and a host of others) and is easily restricted, if somewhat heavyweight. The Lua VM is faster than the JVM, is portable to a number of platforms (having a clean, portable, lightweight implementation), and I suspect that a Javascript front-end would not be hard, given the similarities between the languages (Lua could be described as a cleaner, faster Javascript). The language of choice would be up to the developer, as long as it could target the VM (and we'd not have to put together hacks like minifiers or $language-to-JS compilers like CoffeScript and Objective-J). Getting Google, Microsoft, and Mozilla to agree on a VM is trickier, although I hear MS loves Lua.
I also agree with the app store assessment (1000 suns, etc.), but have little to add.