You seem to be implying that making an effort to seek change in the format that npm uses is a bad idea. I'm not sure I understand why that is. Surely the status quo isn't always perfect?
In the software world in general, and in Node/npm land especially, code talks. I thought it'd be more productive to build and share a working ES5-style JSON parser than to simply ask Isaac if npm would support ES5-style JSON. =)
Yes, you're right about trailing commas. One motivation that such an approach couldn't address is documentation: I've frequently wanted comments in my package.json files, e.g. explaining a particular dependency version, or a script command.