Obito kept a low profile until a lot of Akatsuki had died; in other words, staying relatively out of the picture for as long as he could so as to best ensure Tsuki no Me's success. Using the teleportation ability would've raised a lot of eyebrows amongst Akatsuki, as well as any would-be spies watching their activities from the outside. Besides, teleporting around as a group would slow them down. Even if they managed to retrieve one Biju, the village from which they took it would notice because they're sticking out like a sore thumb.
Then what? The other villages are alerted straight away and the rest are put into hiding ASAP. Hiding in the Kamui dimension? I thought they were supposed to zipping around, instantly knowing where they are and capturing them? Sitting around for hours at a time in the Kamui dimension doesn't match that. Going out as groups of two, they could retrieve multiple Biju simultaneously, but this must come after doing reconnaissance on the location of each Biju, the traps and defences in place, and also the abilities of the Jinchuriki if applicable. All this takes time.
In Kakashi's words:
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