There are two historical elements for why the electoral college was invented. One, discussed by Hamilton in Federalist 68 was to provide a final stopgap against demagogues like Trump http://avalon.law.yale.edu/18th_century/fed68.asp. The second was to give the slave states more power http://www.vox.com/policy-and-politics/2016/11/12/13598316/donald-trump-electoral-college-slavery-akhil-reed-amar and it should be clear why that shouldn't be ok. As for the argument involving counties: that's just silly. There's no reason that amount of total area won should mean anything at all. Moreover, there's no reason you can reasonably object to cities dominating simply because they happen to be dense areas. Disagreeing with a group doesn't mean you get to use essentially arbitrary criteria to decide you'd like to ignore their wishes.
There are good arguments against having the electoral college change in this case (especially given that we don't know if Hillary would have won the popular vote if both her campaign and Trump campaign had optimized voter turnout rather than focused on swing states) but trying to make an argument that relies on county number is just awful.
System checkpoint complete.