Because he seems like he could be either/or, or in between. Because his body turns into actual wax like a Logia type would turn into their element. So far as I have seen Luffy's body stretches like rubber but not actually turn into rubber.
Mr.3(wax) is a Devil Fruit user classified as Paramecia because his body doesn't become that substance but rather gives them an ability to create and manipulate wax. So Mr.3's body doesn't actually turn into wax, he creates and manipulates wax. He doesn't/can't become intangible like Logia users can
I think the wiki will support it. And why would Mr3 need a wax Armor if he was intangible
Luffy's Paramecia because he has a superhuman ability thats odd and again no intangibility
Luffy's body is completely rubber but he can't manipulate rubber (Yet!)
He can use gears because his body is that of rubber (Blood Vessels(2), Bones(3), Muscles(4))
Another such user is seen in Impel Down Arc who has a fruit which may seem as Logia first but is in fact Paramecia
Magellan (Doku-Doku no Mi aka Venom Devil Fruit). He also can't become intangible and Luffy can hit him without Haki. However, his poison can seep through the skin when hit and poison Luffy. Luffy counters this by using Mr.3's wax to go into CHAMPION mode :p (Almost as cool as Nightmare Luffy).
Edit: From the wiki, Trivia
This fruit (About the Doku-Doku no Mi) is often one of the few Paramecia confused as a Logia-class Devil Fruit, because it seemingly produces an "element". However, it is not a Logia because the user cannot transform into the said element, but rather just control it. Despite this, in the anime, Mr. 3 seems to literally melt due to the intense heat of Level 3 in Impel Down, though it is probably intended as a comic effect to get across how much Mr. 3 dislikes hotter environments.
As I said, Wiki basically says the same thing. Mr.3 is not intangible since he is not made of wax and thus not a logia. http://onepiece.wikia.com/wiki/Doru_Doru_no_Mi