You're ignoring that Trump on the ballot meant any Libertarian was going to get a bump. Any other republican, and their winning margin would've been bigger, or Hillary would've won and we wouldn't be having this conversation.
It shouldn't have been close, but the last few elections have been, with the popular vote winner losing the electoral college twice and Kerry coming within ~30 EVs. Do you have a solution for divided media, inequality, climate change, and citizens united, that is simpler than vote trading or making people realize voting for their 2nd preference might just be worth it to hack the electoral college? I'd love to hear it.