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Tobi didn't make a hole in his mask to wield Katons for the same reason he never really engaged in battle much in the first place: He wanted to remain anonymous under the guise of "Madara." His Katons aren't really that important in the long run; with his Sharingan abilities and eventually control of the Bijuu/Gedo Mazou, he was powerful enough to carry out his plans. Once he was un-masked, he used the Katon as a finisher, but it really wasn't that impressive even then.
As for his failure to use the Rinnegan abilities, I believe his usage of the Rinnegan may be handicapped due to lacking both eyes. He probably can't use all of the powers, just as he can't use all of his own Mangekyou abilities. And the Rinnegan abilities could function similar to Susano'o, which requires both eyes active to use.
Obito's Mokuton is similar to his Katon; he hasn't revealed a particularly strong Mokuton, so it's not all that important, although those spears could get the job done. It'd still reveal quite a bit of his overall power, as well as give clues to his identity (albeit small ones to the cast, but big ones to readers).
Franky, I don't think Obito ever really wanted to fight seriously, he just wanted to teleport his enemies to his hidden dimension until he could carry out his plans, killing only when necessary. He still believes he's a "saviour", and while he sees everyone as practically un-real (since they exist in a world he doesn't acknowledge), he still doesn't want to abuse his power just to kill when he doesn't have to.
I believe when the Juubi was first revived, and Madara stated that they had best use the Juubi to wipe out their enemies before carrying out the Moon's Eye Plan, he was expressing some scepticism about Obito's resolve to kill Naruto & Co. To me, it seemed like Madara was thinking the same thing we are, that Obito wasn't really using his full power to defeat the enemies, and things were getting dangerously close to failing because of Obito's weak stomach.
I firmly believe that at the beginning Tobi was indeed Madara - it all fits, he was weak a former shell of himself as itachi said ... gaining EMS granted him amazing powers - space time jutsu ... even his face structure suggested that ... but then Kishi changed his mind and Tobi is ultame recton changer he can blame it all on his lies ...