The "intended" malapportionment to benefit small states[0] is a far smaller effect than the "unintended" effect of silencing local political minorities. If you wanted to retain the former, you could replace the Electoral College with just weighing votes cast in smaller states slightly more. Right now, neither large nor small states have a say in presidential elections at all - it's purely undecided states that play kingmaker, and it drastically warps the priorities of elected Presidents.

[0] Which is also a problem. You know how everyone says the EU is undemocratic? It's for the same reason why we have an Electoral College - the whole "federal government represents states instead of people" thing.