Fix comment regression

It looks like the quick change in 8a9a20512203ed39753af9933c045348110bdd58 broke the comments flag added in #179.

Though, I'm not sure whats going on with this `format` option.

I definitely think comments should be preserved by default. `cat already-es3.js | 6to5 == cat already-es3.js`
We should just set `comments` to default to on here since `_.merge`  pulls in the user's preference.