I don't see a problem with baby skeletons - in fact, I added them to the game to make it more fun, with similar behavior as baby zombies (faster movement and not burning in daylight, which was a feature-turned-bug that was "fixed" in a recent version, but it was clearly intended from looking at the code - so I added it to skeletons as well. Mobs also spawn with armor from head to feet, which was reversed in 1.9 (the Wiki says the opposite so I'm not sure if this is still true), probably to make helmets less likely):
(this is my version of "chicken jockeys")
Of course, they do have the old skeleton AI, where they will stop moving when they shoot, so it is mainly harder to run away from them (notably, creepers used to keep moving while counting down to detonation, which was removed in 1.2, not sure if intentional or not but this makes them MUCH more dangerous - and I restored this behavior, if with a nerf to their peak damage, but it drops off at a slower rate with distance. Many people complain that the game is too easy and/or not exciting enough, so such behavior could be limited to harder difficulties, but I dislike that as well (in particular, try finding armored mobs on Easy in 1.8+ - this is no longer possible due to the fact that regional difficulty (a bad "feature") can't get high enough. I do make the chance of baby zombies/skeletons vary with difficulty though, 5% on Easy, 7.5% on Normal, and 11.25% on Hard, compared to a fixed 5% in vanilla).