You aren't missing out on a "whole lot": You end up being about 80 ADAM down per 3 little sisters, or 320 in the whole game. I'm sure there are 320 atom worth of useless upgrades you don't need to buy in return for some pretty cool bonuses.
This is true... and hell, having saved all the precious little things, I still had a surplus of a few hundred ADAM when the credits rolled. It's not like I was being unduly stingy, either; fights with Big Daddies usually lasted about 10 seconds, and the final boss went down like a chunky street-walker.
The penalty for saving the little sisters really is negligible, and as a bonus, I didn't have to murder a dozen screaming little girls. I consider that a pretty good deal, although I imagine everyone's mileage varies there.