I think people will (and should) continue to use tools like gulp and grunt. They do have the problems you’ve outlined here, but to be fair they’re also both fairly new — it’s amazing they have the proliferation they have.
NPM scripts are great if you know how to write an NPM script. If you don’t, the gulp/grunt APIs are attractive because there’s less overhead to learn. Task running tools are fantastic for Node newbies and people who aren’t interested in learning Node, but still want to be able to benefit from it.