He could have lost FL _or_ OH and still won.
So, did Trump win by a lot when you take out California and New York? Yes. He also lost by a lot when you take out the South. Population is the only fair metric for weighting regions against each other. The South is not entitled to control everyone else's lives, especially since they're the damned region that demanded extra Representatives for their slaves.
Unfortunately, there is no mechanism in place that actively punishes voter suppression. Voters per inhabitant ratio and election turnout could be used to penalize states with low engagement to ensure voter suppression does not occur.
It, however, removes the penalty for suppressing votes because the remaining votes continue to have a fixed weight.
Also, the "CA and NY would run the US" is an extremely weak argument. It's logically equivalent to saying that Texas and Oklahoma are currently running the US, since their electoral votes are sufficient to swap the winner from Trump to Clinton.
Actually, I don't think it's equivalent, since basically no Congressional majority or Presidency has been won without the South for the past 50 or so years. You can actually estimate which party will be dominant in an American party system by looking at who consistently holds the South, irrespective of how other regions vote.
So California and the Northeast can consistently vote one way, and it basically just doesn't matter if the South happens to disagree.