Then you don't understand cause and effect. Firstly, bonemeal is not useless. Just less efficient. Less efficiency means players won't sit and spend as much time spraying their crops with bonemeal. They'll be encouraged to let their crops just grow, since the bonemeal is now a luxury, rather than something incredibly common. It follows a chain of events, let me explain:
Pre 1.5 bonemeal:
Player kills a single skeleton easily, gets a bunch of bonemeal for it. Player gets a tiny bit of experience.
Player goes and grows crops, makes bread.
Player has plenty of bread now. Player doesn't need more wheat, so they aren't likely to want more bonemeal yet.
Post 1.5 bonemeal:
Player kills a few skeletons, which are now tougher. Player gets a little more experience because they killed more skeletons.
Player goes and encourages crop growth, makes a little less bread than before.
Player needs more wheat. Player goes and repeats the process. Player gets more experience, because player needs to kill more skeletons than they did before. Or, player decides bonemeal isn't worth the time, so player goes and does something else while their crops grow.
I have deduced both chains from personal experience.
I beg to differ:
Player kills a single skeleton. Player gets, on average, a SINGLE loaf of bread. Player doesn't starve early on, and goes on to mine and explore.
Player nearly gets slaughtered by new "murder skeleton". Assuming they survive, player goes and grows a single piece of wheat. Player says, "I'm not going to get myself nearly killed fighting 2 more skeletons for a single loaf of bread! Player decides that bonemeal is USELESS and let's their wheat grow naturally.