Some of the same countries that offer partial or full legal protections for transgender individuals also have excellent colleges and universities. That's why Western Europe on this thread. I have also heard good things about Canada.
I live in the US. I would describe transgender protections here as ok but not great. Some areas/states within the US are pretty good but you would be dealing with the federal/national government to obtain citizenship, and those policies might be better or worse in the future when you apply. Several other countries are further ahead.
Another thing to consider is health care. If you do qualify in the future to become a citizen of a different country, does that country consider health care to be a fundamental right of all citizens or not. In the US you would be relying on private insurance. The US has some of the highest costs in the world for medical procedures. I am probably going to travel to Spain for my Facial Feminization Surgery.