I think that Rubio would have beaten Clinton. The electoral margin may not have been as large, but he would have won the popular vote because he would not have done a lot better in California and Texas than Trump. Third party voting would be lower because Republicans would have an easier time getting behind Rubio.
Rubio: 288
Clinton: 250
His appeal amongst affluent voters gives him Virginia, and his appeal amongst Hispanics gives him Colorado and Nevada. However, he would be weaker amongst white working class voters than Trump, so he would not win Wisconsin, Michigan, or Pennsylvania. He would still win Ohio and Iowa.