Giving herself a penis instead of a vagina should've been an easy decision. No more periods? Who could say no to that? Strangely, Yuki did. And it's not like she hated having a penis in Josh's life. She was perfectly happy being a dude as Josh, just as she had always been perfectly happy being female as Yuki. But, Josh had been attracted to Yuki's body, enough to merge their minds together and inhabit her body. That included her vagina.
Granted, Josh had previously made himself bi, and by extension so was Yuki, now. So this body would likely be just as attractive with a penis as a vagina. But now she could explore her sexuality from a female perspective.
She then realized, with a blush, what that would mean. (A blush that was even visible in her mouse ears.) Josh had always imagined getting intimate with Anna's friends, and he had imagined doing it with a penis. But now, she was very much female. That would make for a much different encounter than she had imagined. Meanwhile, before the merge, Yuki had always been straight, so she likewise never considered a lesbian relationship, even with how tightknit she was with her friends. And now, thanks to the merger, she was engaged to one of those friends. Memories of falling in love with Anna and getting engaged were now mixed with memories of Anna being one of her besties.
On top of that, Anna was now a male tiger named Andrew. A male who was now bi like her. Before the merging, Yuki was never able to get a boyfriend because she was too shy. Yet she always dreamed that she would one day meet Mr. Perfect, maybe even start a family. With Josh's personality now being the dominant one, she wasn't sure she still wanted to become a mother. But her interest with meeting Mr. Perfect aligned perfectly with her love for Andrew, and she found herself hoping that perhaps Andrew would want to become her husband instead of her wife. A very surreal hope, given the circumstances. But one that Yuki was relishing.