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Seriously, who came up with the idea of making so many Zubats?
Looking their movesets, it really looks like they're made to be a pest.
A level 11 Geodude learns Rock Throw which is almost a guaranteed OHKO against Zubat. Most of Zubat's attacks do nothing to Geodude as well, except for Sonicwave with its confusion. Of course you'll likely have to wade through a few Zubat's to even run into Geodude.
A decent leveled Pikachu is also a thorn in their sides with Thundershock and are usually fast enough to go before Zubat. This will probably be the better choice while looking for Geodude at least. Considering you can catch Pikachu pretty early and fight mostly flying types before reaching the cave, it should be properly leveled. ;-)