You're ignoring that these smaller populations have fuck all in power that urban centres do, as urban centres are already where most all power resides
Power is already consolidated amongst too few, you want is consolidated amongst even fewer. This is reckless, dangerous and there is no reason why rural populations should stand to obey such a system except with their physical subjugation, otherwise they have nothing. Urban centres decide all things academic, thus they control the future ideologies of the nation. Urban centres decide all things financial, thus they decide where all money goes in the nation. Urban centres are most of the economy itself. They decide the media, the popular culture that defines the nation for such heavy influence. They are the most interconnected, lines of communication smallest, elites most well-connected; giving them guaranteed victories in every election is gamebreaking more than the game is already broken
And you're ignoring that urban populations are currently the ones being disenfranchised, a great portion of the time, with various methods to make it more difficult to vote.
More relvantly, however; if urban centers control all academia, and academia is liberal, and that in and of itself automatically decides future ideologies, rather than merely having an influence, then Trump would never have been elected.
What you are saying amounts to 'There are a lot of them, therefore those people have votes which are worth less'. Literally you're saying they should have less of a say because we should not use flat population counts. And your reasoning for this is that those people have no effective wills of their own, and are simply controlled by the elites. And yet that becomes less and less true, even in the indirect sense, as time goes on and information becomes more readily accessible. Unless, of course, you believe the media conspiracy has become all-encompassing.
Presidential elections being decided by popular vote does not usher in a new reign of cyberpunk darkness. There will always be an arms race between parties to secure votes. Even were you right about what and how it would play out, rebel factions would still spawn within the democrats and split it into new parties, and each would end up aligned with the results of around half the country, because when you manage to split the urban vote, the rural vote matters, even if it's small. Society is an organism, or an ecosystem, not a finely-tuned machine, and though an ecosystem can certainly desertify, well...
You've been talking a lot about Empires falling lately, comparisons to Rome a fair amount though that was a while ago (to be fair you haven't said anything explicitly about Empires in at least a few weeks, I think, but still). Thing is, I really like the Eastern Roman Empire, sometimes known as the Byzantines. They're fucking cool, man
kataphractoi are the shit ANYWAY. I've been reading about them, and the thing is, Roman Empire came very close to falling on several occasions. And it came back on each but the last, and even then, there's a fair chance it would have except the guy who could've brought it back got shanked by his own soldiers because he decided to be diplomatic with some barbarian tribes instead of kill them (you know, the thing that let Rome actually survive and prosper so long; buffer states and shit).
So...really don't think 'direct popular vote' instead of 'multi-tiered FPTP popular vote' for the executive office will spell the doom of society and rural folks as we know it.
Really though the solution is next new deal focusing on rural and depressed economic areas, with raised taxes on rich, closed tax loopholes, and maybe even trade barriers specifically on MNCs that decide to try and move overseas to avoid taxes (or just specific taxes so they still get hit with 'em). Maybe Trump will go down in history as having that become his thing, and get four more years by being successful.
Hell of a lot better than a civil war from him getting assassinated, Mike Pence taking office, and riots ensuing from everyone everywhere simultaneously.