What am I allowed to think about in the bathroom? Are thoughts of desiring to finish Shas permitted? What about thinking of negative traits I would like to improve? Is there anything else that is allowed?

The prohibition of Torah thoughts in the bathroom is in Torah itself or in things which will lead to thoughts of Torah such as grammar of the holy language. Thoughts about spiritual aspirations or character improvement are permitted and even to be encouraged. The Mishnah Berurah notes that it is clearly permissible to contemplate his lowliness in the bathroom, and that he will eventually return to dust, worm and maggot, and that arrogance is not becoming to him. The Mishnah Berurah suggests that he should think of his financial affairs and expenses in order to avoid thinking Torah thoughts, and on Shabbat he should think about nice buildings and paintings. [שו"ע או"ח סימן פה סעיף ב, ומ"ב ס"ק ה ו].