This election was anomalous in many ways. The approval ratings of both candidates were historically low. Perhaps related, third-party candidates were garnering much more support than usual. The nationwide polling of Gary Johnson was close to 5% and Evan McMullin was polling close to 30% in Utah. There's never really been a candidate without a political history who has gotten the presidential nomination of a major party and there's never been a female candidate who has gotten the presidential nomination of a major party.
These anomalies certainly make statistical predictions more difficult. We'd expect that a candidate might perform similarly to past candidates with similar approval, similar ideologies, or similar polling trends, but there were no similar candidates. We have to assume that the trends that carried over in past, very different elections apply to this one, and presumably, this is why so many of the election prediction models were misguided.
I have a few thoughts I wanted to write out. I am in the process of collecting more data to do a more complete analysis.
Did Gary Johnson ruin the election?
No. In fact, evidence points to Johnson helping Clinton, not hurting her. Looking at the predictions and results in many of the key states (e.g. Pennsylvania, Michigan, Florida, New Hampshire; Wisconsin was a notable exception) Clinton underperformed slightly compared to the expectation, but the far greater effect was that Trump overperformed and Johnson underperformed compared to expectation. This is a pretty good indicator that those who said they'd vote for Johnson ultimately ended up voting for Trump. There seems to be some notion that people were embarrassed to admit they'd vote for Trump in polls. This might be true (but also see this), but the fact that third-party candidates underperform relative to polling is a known effect. However, the magnitude was certainly hard to predict because a third party candidate has not polled so well in recent elections. It doesn't really make sense to assume Johnson voters would vote for Clinton either. When Johnson ran for governor of New Mexico as a Republican, he was the Libertarian outsider, much like Trump was an outsider getting the Republican nomination for president. Certainly, Johnson's views are closer to the conservative agenda than the liberal one.
Turnout affected by election predictions
There has been reporting on how Clinton has gotten the third highest vote total ever of any presidential candidate (after Obama 2008 and Obama 2012). This is a weird metric to judge her on considering turnout decreased compared to 2012 and Clinton got a much smaller percentage of the vote than Obama did in 2012. Ultimately, the statement is just saying that the voting pool has increased, not any deep statement about how successful Clinton is. In particular, let's focus on the 48% of the vote that Clinton got. I have to imagine that if there is a candidate with a low approval and there are claims she has a 98% chance of winning the election, that a lot of people just aren't going to be excited to go vote for her. I could see this manifesting as low turnout and increased third-party support. Stein did do about three times better than she did in 2012 (as did Johnson). In addition, people who really dislike the candidate (and there are a lot of them since the candidate has a low approval rating) are encouraged to show up for the election. I don't see obvious evidence of this, but I have to imagine there was an incentive to go vote against Clinton. This could explain the slight underperformance relative to polls in the aforementioned states as well as the large Clinton underperformance in Wisconsin. There's been talk of fake news affecting the election results but I think the real news predicting the near-certain election of Clinton had just as much to do with it.
Would Clinton have won if the election were decided by popular vote?
This is a very difficult question to answer. The presidential candidates campaign assuming the electoral college system so clearly the election would be different if it were decided by popular vote. Certainly, this seems quite efficient for Democrats. Democratic candidates can campaign in large cities and encourage turnout there, whereas Republican candidates would have to spread themselves thinner to reach their voter base. One thing I haven't seen discussed very much is that this would probably decrease the number of third-party voters. In a winner-takes-all electoral college system, any vote that gives the leading candidate a larger lead is wasted. So, in states like California, where Clinton was projected to have a 23 point advantage over Trump, a rational voter should feel free to vote for a third party since this has no effect on the outcome. In a national popular vote, there are no wasted votes and a rational voter should vote for the candidate that they would actually like to see be president (of course people don't always act rationally). As argued before, Johnson's voters seem to generally prefer Trump over Clinton, so the number of these people that would change their vote under a popular vote election is definitely a relevant factor in deciding whether a national popular vote election would actually have preferred Clinton. Stein's voters would generally prefer Clinton over Trump, but there were fewer of these voters to affect the results.
Electoral college reform needs to happen
Yes, but if it didn't happen after the 2000 election, I think it's unlikely to happen now. The most likely proposal that I have been able to come up with (with the disclaimer that I have very little political know-how and am strictly thinking of this as a mathematical problem) is to increase the number of house members. This is only a change to federal law, and thus would not be as hard to change as the whole electoral college system, which would take a constitutional amendment. If states had a proportional appointment of electors, then as the number of house members increases, the electoral college system approaches a national popular vote election. This is complicated by the winner-takes-all elector system most states have. For example, the total population of the states (and district) Clinton won seems to be 43.7% of the total U.S. population, so even though she won the popular vote, with winner-takes-all systems in place, it is difficult to imagine a simple change to the electoral college system that is closer to a popular vote.