Sometimes I will see one of those "LGBT-friendly city" lists, and they always make me roll my eyes. Trans people are usually looking for specific types of trans-related services such as ample choice of therapists, endos, and possibly surgeons, as well as community and support groups. We look for what LGB look for, sure, but T is a lot more complicated. I have never seen a "top ten trans-friendly" list, but maybe I missed it.
I do remember cities such as Seattle, Denver, and Portland, OR, on those LGBT lists. I believe that these cities are pretty affordable and accepting, and they should have the services we usually want, but you would need to do more research. Most people will also mention SF, LA, and NY. I understand that all three of those cities are very expensive to live in, though. I should think that almost any city in the top ten or twenty in population would be large enough to have the infrastructure you need and would be worth at least some research.
One thing you ought to take into consideration is connections. In which cities, if any, do you have friends or supportive relatives or colleagues? If you work for a national company, where can you transfer to? If you have a particular profession and not just a job to pay the bills, which cities best support that profession? And for some folks, where do you want to go to school, or what if you decided to go back to school?
Another possibility is to live in an area very close to one of the hubs. For instance, some people don't mind living in less desirable areas (read: cheaper) in CA and driving a bit to get what they need (work, trans services, or both). But the areas they live in are often less accepting. I have the good fortune to be able to do the opposite--live in a progressive area but work in a progressive school in a less accepting area. So I pay more for living expenses, but I have decided that it's worth it. Doing what I do is a possibility for folks in some professions. But a truly reliable car, and the willingness to perform regular maintenance, is an absolute necessity for most people in either of these two scenarios because of the commute.