why was she never in Karate Kid II?

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I don't know this for a fact it's seems obvious they needed some sort of love interest for Daniel, but being set in Japan they couldn't just have Alley tagging along so they rid of her with Daniel's prom story of how they got in a fight and boom, all clear for someone new.

My opinion is that she wasn't available to do the sequel.
She did a TV movie entitled,"Call to Glory' and that TV movie was made into a TV series that had 23 episodes.That was made from 1984 to 1985.
She probably got very busy and wasn't available.
In Karate Kid II,it was explained that her character,Ali took off with her football player and left Daniel after he won the competition.

actually she went out with Snake who would later emerge in Part III

http://www.mickey-rourke.com/

Dude, you rule IMDb. The end.

"Martha is 108... years old. She weighs somewhat more than that". - George

She didn´t leave him right after he won the competition. It was 6 months later, right after their prom and right at the end of their Senior year, right before Daniel left with Miyagi for Japan.