Your second reply hadn't appeared when I was typing my last, so apologies for "dodging" the question about how to improve the system.
In fact the Electoral College (EC) probably makes it easier to lock in the two-party system, rather than harder, so the solution is simple: get rid of it. The primary purpose of the EC was, anyway, nothing to do with political parties but all about trying to balance the rights of small states against larger ones. This is, though, already achieved by the make-up of the Senate (two members per state, regardless of size) and House of Representatives (somewhat, but not exactly, proportional to population), while anyway States also have other constitutional rights protecting the smaller ones from imposition by larger ones.
That is to say, the problem that the EC is meant to address doesn't really exist. A president could therefore be elected directly by popular vote without undermining the principles of the US Constitution.
So far there has only been one election (in modern history, ie since WWI) where a third-party candidate had a decent shot at winning, that being 1992 when Ross Perot ran. I don't think he would have won even without the EC, but one wonders how much of a difference it would have made to his chances had the wave of popular support he enjoyed not been impeded by EC considerations. In the event, Perot received almost 20 million votes and got exactly nothing in the EC, while Bush Sr. received only 5 million votes less than Clinton but got less than half of the EC for his troubles.
But apart from 1992 (and, to a lesser extent, 1912), third-party candidates have been virtually absent -- and, more to the point, even when they have done relatively well in the popular vote, they have come absolutely nowhere in the EC. It's therefore a mistake to claim that the EC in any way has enhanced the prospects of third parties.