In my opinion the best system for US presidential elections would either be a nationwide instant-runoff election or (if the electoral college couldn’t be replaced) a state-by-state single transferable vote election that proportionally elected Electoral College electors.
An instant runoff election would let voters put Johnson or Stein as their first preference and put Clinton or Trump as their second or third preference. It completely eliminates the problem of spoilers. The counting of votes might take a bit longer (perhaps a day or two if done manually), but needing to know the result within a matter of hours isn’t a requirement.