This is why I'm looking forward to the Edge w/ its Ubuntu OS. It doesn't try to hide its Android heritage, even gives you the option to boot to AOSP. Also has a modern gesture based UI unlike Firefox's dated iOS rip off. And most importantly, on resource limited mobile device gives developers the option to write native apps.
[1]http://www.theverge.com/2013/2/24/4024530/ztes-open-is-the-f....
[2]http://reviews.cnet.com/smartphones/geeksphone-keon/4505-645....
> I also wonder about the wisdom of taking low-end hardware, where every bit of efficiency at the software level matters, and shackling it by not allowing third-party native code.
This is what asm.js and OdinMonkey are for. You're right that forbidding developers from getting the control that native code buys you is a nonstarter, but asm.js gives you that control.