Wait, if POPs just care about how much money they are actually paying and low tax efficiency only makes them pay less, then what's the point of tax efficiency? Why would you care about increasing it if you just have to raise the tax slider to get exactly the same effect? Unless you want to raise taxes over the tax efficiency percentage, of course, but if the game is anything like Vicky 1 after you get, say, 50% tax efficiency you probably wouldn't want to raise it even more due to high MIL increases and people leaving your country. Is there any advantage at all in increasing tax efficiency once you get to the point where setting your taxes at 100% gives you the actual desired tax rate?
What I would do would be adding corruption into the game. Maybe some of the "lost" taxes should remain in the taxpayer's hands, but a big chunk of it should end in the pocket of aristocrats and/or bureaucrats (depending on your government type). And of course POPs should get the full MIL increase from the money that was stolen. Or, to make things a bit more complicated, you could add a "corruption" value which would determine the percentage of the lost money which remains in the taxpayers hands and the percentage of it which would be stolen. You could then tie this value to some of the requeriments for westernization or do further interesting things with it, and you'd decrease it by assigning money to the equivalent of Vicky's crimefighting.
Something to wish for in an expansion, I guess. At least the first part...