I've recently started looking into Ember - which of their framework decisions do you dislike?
I prefer mocha to qunit and I'm a fan of coffeescript (ES6 can wait. I love the existential operator). My company had made a few decisions before ember-cli that weren't on the Ember Happy Path. I've tried to stick to those decisions to avoid making people learn a different stack. It's not that easy to rip and replace pieces of Ember.
I think having a cli will become standard for JS frameworks. You just need to have the batteries included to capture the newb mindshare.