The Google Script will save any Gmail message (or thread) in your Google Drive as a native Google Document with proper formatting. Unlike the Save Gmail as PDF script that downloads the email threads as PDF files in your Google Drive, this Google Script create a Google Docs file for your Gmail message and these do not count against the storage quota.

function saveGmail(msgID) {
  // Based on Drive Scoop
  // Available at https://github.com/google/gfw-deployments

  var message = GmailApp.getMessageById(msgID);

  // Grab the message's headers.
  var from = message.getFrom();
  var subject = message.getSubject();
  var to = message.getTo();
  var cc = message.getCc();
  var date = message.getDate();
  var body = message.getBody();

  // Begin creating a doc.
  var document = DocumentApp.create(subject);
  var document_title = document.appendParagraph(subject);
  document_title.setHeading(DocumentApp.ParagraphHeading.HEADING1);

  var style = {};
  style[DocumentApp.Attribute.HORIZONTAL_ALIGNMENT] = DocumentApp.HorizontalAlignment.CENTER;
  document_title.setAttributes(style);

  var headers_heading = document.appendParagraph('Gmail Message Headers');
  headers_heading.setHeading(DocumentApp.ParagraphHeading.HEADING2);

  AddGmailHeaderToDoc(document, 'From', from);
  AddGmailHeaderToDoc(document, 'To', to);
  AddGmailHeaderToDoc(document, 'Cc', cc);
  AddGmailHeaderToDoc(document, 'Date', date);
  AddGmailHeaderToDoc(document, 'Subject', subject);

  var body_heading = document.appendParagraph('Body (without Markup)');
  body_heading.setHeading(DocumentApp.ParagraphHeading.HEADING2);

  var sanitized_body = body.replace(/<\/div>/, '\r\r');
  sanitized_body = sanitized_body.replace(/<br.*?>/g, '\r');
  sanitized_body = sanitized_body.replace(/<\/p>/g, '\r\r');
  sanitized_body = sanitized_body.replace(/<.*?>/g, '');
  sanitized_body = sanitized_body.replace(/&#39;/g, "'");
  sanitized_body = sanitized_body.replace(/&quot;/g, '"');
  sanitized_body = sanitized_body.replace(/&amp;/g, '&');
  sanitized_body = sanitized_body.replace(/\r\r\r/g, '\r\r');

  var paragraph = document.appendParagraph(sanitized_body);

  document.saveAndClose();

  return document.getUrl();
}

function AddGmailHeaderToDoc(document, header_name, header_value) {
  if (header_value === '') return;
  var paragraph = document.appendParagraph('');
  paragraph.setIndentStart(72.0);
  paragraph.setIndentFirstLine(36.0);
  paragraph.setSpacingBefore(0.0);
  paragraph.setSpacingAfter(0.0);
  var name = paragraph.appendText(header_name + ': ');
  name.setBold(false);
  var value = paragraph.appendText(header_value);
  value.setBold(true);
}