Which less-populated areas are "irrelevant"? Wouldn't the same reasoning apply to the current system, just on a state-wide level: the handful of metropolitan areas make the votes from other areas of the given state irrelevant?
I also still don't see how, considering that Clinton only got 6 million more votes than Trump in California and New York, those 2 states would control a popular vote election unless, maybe, the voters all went for a single candidate.
Metropolitan areas are always going to have an advantage over rural areas in terms of numbers. That's a given. However, there's a big difference between a state's electoral votes leaning toward its biggest population center and the entire nation's election being controlled by a handful of cities. For starters, the people of southern Arizona have a lot more in common with the people of Phoenix (I use this example because I live in Arizona) than the people of Arizona have with the people of New York City.
That still does not answer the question of how those states control an election by national popular vote. If anything, those states would grant less influence to one party with a national popular vote. As it stands, all of the electoral votes in Cali and NY go to the candidate with a plurality in each state. So those metro areas are already having a larger influence than they would with a popular vote, because the votes for losing candidates are ignored on the national level; if the metro areas control the vote, they are already giving every electoral vote to the Democratic candidates, and have done so since the 80s.
How would "a handful of cities" control the nation's election? Again, there were near 130,000,000 votes cast in the 2016 election. How many of those votes were from the cities in question, and did all of those cities vote for the same candidate?
The idea that a small number of cities will decide every election is tossed about like a fact, but I have never seen any statistics to actually back up the claim.
There are certainly issues with a national popular vote for president. That a handful of cities would control such a vote is not, I think, one of them.
Of course, it's possible that a national popular vote would cause a radical shift in the voting habits of the public which would render all I've said moot.