It makes as much sense as the way it's done now. Maybe initially they wanted everyone to participate and that still makes sense for amateurs. But in the highest professional league it's all about entertainment and there is nothing entertaining about watching the bottom of the batting order.
Now the best way to deal with that is to simply have only six men bat, eliminating the bottom three. Everyone plays the field but only six bat, the minimum without a player coming to bat with himself on base. I've advocated that from the first Radical Baseball writing back in 2006.
This is an alternative way of approaching it but with an attempt to rewrite history and correct bad judgement. There would be some additional tension as a team works its way down the batting order and approaches players who bat much less frequently. If only we can get past them, the players who are much better can get up again this inning and prolong a rally.
The top three especially would bat much more often, maybe almost twice as often as those at the bottom. A team could toy with the idea of having fielding specialists at the bottom and take the chance that they would seldom need to come to the plate. You know, like pitchers for over a hundred years.