There's probably a better place to ask this question, but I don't know what it is. That being said...
Which will go further if a batter manages to hit it with a baseball bat: a baseball thrown to the batter at 90 miles per hour or one thrown at 60 miles per hour?
No reason to be confused, remember you have ignored the force exerted by the batter. If the ball is enough heavy and fast, it will simply shoot away the bat and continue forward. (Edit: the mistake you made is
which you can't, since the posterior bat velocity isn't independent of the prior ball velocity.)
Let's make it explicit:
Let w and W are velocities of the ball and the bat after the hit, v and V are the velocities before the hit, m and M are masses of the ball and the bat, respectively. Then we have
v+2MV}{m+M})
This means that if the bat is ligther than the ball, the faster you throw, the slower the ball returns, or it doesn't return at all, if 2MV is lower than (m-M)v. On the other hand, if the bat is heavier than the ball, the faster the ball moves initially, the faster it returns.
Of course, one shouldn't disregard the batter completely. A better model is to assume that part of the batter is co-moving with the bat. Then, M is the aggregate mass of the bat and the movable part of the batter, which is very likely to exceed the mass of the ball, and then, the faster the ball goes, the faster it returns.
Even better model expects that part of the energy is lost on the bat-batter boundary and in the batter's muscles and joints. Now we should have a reasonable model of how much this is. My hunch is that this amount in fact increases (absolutely, not only relatively) with increasing speed of the ball: if the ball is really fast, it will knock the bat out of the batter's hands before the impulse could be transmitted between the batter's body and the bat, making it effectively a free bat and ball system. But I don't have any idea about actual numbers.
By the way, I envy you Americans such a Newtonian sport. It's not so easy to modify those examples to naturally fit soccer or ice hockey.
Edit: I have now found that the bats are a lot heavier than the balls, which makes all speculations about the batter's physiology irrelevant to the question.
Intuition pump: if the masses are equal and one isn't moving, then as per a Newtonian cradle, the moving ball stops completely and the other takes up its motion.
Also, hooray for Maxima!