jQuery templating with ES6/ES2015 template strings
I was reading through your code and I got to 


  if(value) {
    if(value instanceof Node || value instanceof jQuery || allNodes) {
      nodeIndexes.push(i);
      html += tempFiller(i);
    } else if(value) {
      html += value;// || '';
    }
  }



and I had to read over it a few times, but I think that you can do away with the outside if statement or at least not check value a second time.  

either one of these look like they are going to do about the same thing

if (value instanceof Node || value instanceof jQuery || allNodes) {
    nodeIndexes.push(i);
    html += tempFiller(i);
} else if (value) {
    html += value;
}


this would go through both checks, much the same way that the original code did, except you don't check the existence of value first, this might cause some errors, so I would probably do this instead

if (value) {
    if (value instanceof Node || value instanceof jQuery || allNodes) {
      nodeIndexes.push(i);
      html += tempFiller(i);
    } else {
      html += value;
    }
}


turned the else if into an else, because we already know that value is going to pass a truthy test, no need to check it a second time.