Your point makes so much sense that it must be the standard in all of the other states, right?  And it is!  That's why California's capital is in LA, New York's is in NYC, Colorado's is in Denver, Washington's is in Seattle, Texas' is in Dallas...  If state capitals were in the areas with the highest population, those highly populated areas would completely forget that the rest of the state exists.  

You can pull the capital out of Juneau and destroy the economy of the state's third largest city and the entire region, if cannibalism is what you're into.  But if you really want to save state money, stop sending the usual caste of crooks and fools to Juneau.

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