The problem with properly evaluating Aldridge (or any player, really, but Aldridge seems like one of the more complicated ones in this regard) is determining just how valuable he is on defense. While I hardly think PER is the be-all and end-all in terms of measuring production, I think it's a pretty good quick look. Defense, however, is still pretty dicey in basketball, since it's so team-oriented (baseball, for example, is a largely individual pursuit in the guise of a team sport). I think if you asked 100 different basketball observers to watch Aldridge play defense all season long and decide, without conferring, how valuable he was on that end of the court, you'd get some wildly differing answers, running from not too good to mediocre to quite good. You might even get some people who felt he was really valuable.
I think Aldridge tends to be a bit underrated defensively. He's not a blocks or steals machine, but he's a solid man defender and a good help defender and he's very versatile...he can jump out on a wing for a short time and not have it be an automatic negative defensive result, in addition to defending both front court positions capably.
Of course, that's just my opinion. But that's why I don't find it implausible that he could be between Stoudemire and Howard in terms of total value.