The Tigers might very well feel that it's harder for them to acquire quality pitching than it is to acquire quality hitting, and thus quality pitching is more valuable to them. If you look at the Brewers top prospects, that same thing could be said about the Brewers.
I think we also may be over-valuing Pena relative to the industry. Pena had some unknown health scares, some minor injuries, and hasn't yet shown that he can make the jump to AA. There is upside, but there are also are risks with him, and risks lower value.