Again, you figure out which one does more to help their team win
It doesn't matter what the answer is so much as the process of asking the question
To say we shouldn't even bother with any analysis because they don't play the same position is far different
So often comparing things that do not appear similar is actually a far better way to learn and understand things. It's very easy to see that Derrick Rose is better than an average point guard in 2011 (say Earl Boykins) -- they play the same position in the same era. Now compare him with an All-Star forward or center from the 70s. Of course it's harder. But that just means you actually have to ask exactly what it is he does well on the court that is so good (and what he does that is limiting). Anyone who refuses to even look at those sort of questions will not understand the sport very well
I'll take Howard over Rose
Hell if you want, comparing them to players of the same position can be ok enough. Can't see any centers even coming close to Howard this year; strong arguments could be made for Williams, Westbrook and Paul at point guard