That "structural favouritism towards less populated areas" is a very old design feature of American democracy. Without it, everywhere but a small band in each coast would become politically irrelevant, much like it's already ignored by the media.
Clinton's projected by the NY Times to win the popular vote by 1.2% right now. That's hardly a huge mandate for a singular agenda. It's a margin that would still be at massive risk if people continued ignoring those non-coastal populations feeling economically left behind.
Instead, despite that 1.2% lead for the Democratic presidential candidate, that party will be the minority party in every branch of government? That's a better, fairer system?
Structurally separating everyone into groups drifting further and further apart for everyone is a recipe for a system that can't get much useful stuff done.
(And the media ate up the Trump campaign despite it being incredibly unappealing to those small coastal bands. Nobody build an unassailable media monopoly by ignoring something like 48% of the population.)
She campaigned for the electoral vote, not for the popular vote.
You can't be sure that if, instead, the popular vote were used that she would have taken a different platform that was soundly rejected by most states but secured her a much larger popular vote margin.
