I think smallness of sample size makes makes the difference appear a bit more stark than it is with those two pitchers.
I'd also agree that putting Smoltz and Penny in the same comparison won't be viable much longer as their national league samples grow down the stretch this year. The Dodgers are excited that Penny appears to be lined up to pitch against them twice down the stretch.
That said, a look at the comparative figures between the two leagues will support Roy and others' assessments that yes, there is a significant difference between the two leagues, hitting-wise. AL teams average a .765 OPS against .742 in the NL, and MLB's top four run-producing teams as well as seven of the top 10 are from the American League.
As several have pointed out here already, given the differing rules in the two leagues, that shouldn't be a shock.
On the flip side, of course, NL pitching averages are a bit better - but just like with hitting, they aren't exactly fair "better-worse" comparisons, because both sides are playing with different rules.
-sw