Maya's obj/mtl import is very poor when it comes to assigning materials to objects. It reads and creates the material shaders but does not assign it to the imported objects.
Other apps including 3DSMax and Lightwave can read in the same obj/mtl files and assign textures.
For years obj/mtl was the so called import vehicle for Maya, and it never worked the way it should have.
Now that Alias is pushing the FBX scheme for exchanging data I suppose the obj/mtl import problem will never be fixed.
Unfortunately, FBX is more for exporting from Maya to other apps more so than importing. If I export FBX from Maya to Max, then great, its painless with only a few material attribute problems. If I go from Max to Maya, then I often end up with models that can crash Maya (duplicate shading networks, meshes with invisible defects). Imports sometimes take forever and result in a textured model that looks good but causes the display to slow down to a crawl (it should not). Then if I take that mesh and add it to a new layer, my system memory quickly goes down to nothing. Crash and burn.
Obviously a serious problem with the FBX import into Maya. Since Alias wrote both the Max and Maya plugins (and I'm using the latest versions of both), you cannot point a finger at Discreet.
Sorry, to rant. I've waited for years for Maya to fix the texture mapping on the obj/mtl import. So many articles and web links on this subject and no answers except to use third-party tools.
Oh, did I forget to say that Maya doesn't write good obj/mtl files. Same texture issues.
No product is perfect when it comes to import/export (there are many technical issues), but I really dispise the fact that I have to spend so much time to get a textured mesh from another application into Maya. The 3DS format is probably the best way although the meshes are hard edged and faceted.
FBX needs serious work, and who will support it since Alias bought Kaydara.