Well, as picky as I am, I consider WW Link and Paper Mario to be two different scenarios. From the perspective of their creator, Miyamoto, Paper Mario is the same character is the Mario from Galaxy, Sunshine, 64, etc. Case in point, there is only ONE Mario.
Now, Miyamoto created Link with a story that spans many different (but similar looking) characters. WW Link fighting against TP Link almost makes sense, because they aren't the same entity.
Edit: I just realized that my mind has been exploded . . . I forgot about the whole 'insert sexual reference with my brain here' that is Adult and Young Link in Melee . . .
. . . curse you, Sakurai . . . curse you . . .
Re-edit: A chance to redeem myself from my last pathetic edit! I suppose, the situation between Adult and Young Link's (both being from Ocarina of Time) could be compared to Mario and Paper Mario, but the fact still remains that TP Link does not equal WW Link. I know it's just semantics, but hey, I like 'em.