I think this focuses on a particular form of identity i.e. the state a person belongs to but ignores other dimensions like race, gender, age, etc. Yes California would have more power under a popular vote than it does today and smaller states would have less, but a popular vote would increase the value of different dimensions of identity like race for example as Mormon voters and Black voters would get an increased influence.
Furthermore, increasing the value of these different dimensions of identity changes the incentives of politicians, so maybe state identity becomes less salient and thinking of voters in different ways becomes more prominent. It is not obvious what would happen, but the fact is that the Electoral itself overweights certain states beyond others, giving some all the power today.