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My understanding is that the force seeks balance. As Yoda is essentially one with the force now, he can only act within the confines of that balance. The turmoil within Luke regarding the temple/tree was throwing the force out of balance so Yoda acted as the force as a whole and restored balance. He did not utilize his own force powers to summon lightning, he acted as more of a messenger of the force.

While I have a good deal of issues with the movie and with Rian Johnson's handling of logic (which was also an issue in Looper), this isn't really one of them.