The idea of emancipation is pretty appealing to most 16 year olds. Just on a first read of your post what I get is that you don't want your mom to be able to interfere with you dating another person more then anything else. That argument has gone on as long as there have been parents and teenagers, Shakespeare obviously wrote about it.
So my short answer is No.
From Wikipedia:
"The exact laws and protocols for obtaining emancipation vary from state to state. In most states, the minor must file a petition with the family court in the applicable jurisdiction, formally requesting emancipation and citing reasons why it is in their best interest to be emancipated. The minor must prove financial self-sufficiency. "You said your plans are to stay with someone over the age of 18 who is renting an apartment (or who at least has the ability to rent an apartment). Make sure that everyone's name is on the lease. It's not like owning a house, they can't just take in every stray that shows up on their doorstep. The apartment will want your particulars as well so they can judge how likely you are to care for their property. Further, the occupancy is often limited by the number of bedrooms, for three people to live in an apartment, they will likely only rent you a two bedroom apartment, for which in an average market I paid my share of about $850 about six years ago. Try to cheap out and it's likely your neighbors aren't going to be any more tolerant of your transition then your mother is. Thinking about moving in in the middle of the night and staying off the lease? Great way to get everyone evicted for breaking the lease.
Speaking of roommates, it wouldn't be the first time someone collected the rent from their roommates, appointed themselves responsible for paying the rent and never did. "Jointly and separately" means you're all responsible for the rent, they don't care that you forked over your hard earned money to your roommate, who despite his best intentions to pay the rent didn't – you're all out on the street. I've had two roommates, one I'm no longer friends with and the other one I very nearly cost myself a friendship. You can be best of friends, but it's a whole different matter when you live together. Especially someone you think you might be getting romantically interested in, I've been down that road.
"Emancipations are not easily granted because of the subjectivity and narrowness of the definition of "best interest." Some are minors who have been victims of abuse. In most cases, the state's department of child services will be notified and the child placed in foster care."Foster care is the last place you want to try to transition while the court system sorts out your petition. In short, it's not going to happen. Child services takes a dim view of children wearing clothes of the opposite gender, any foster parent is not willing to risk their license to be accused by CPS of breaking the rules (which forbid forcing a child to dress in clothing of the opposite gender as punishment)
Others are minors who are seeking emancipation for reasons such as being dissatisfied with their parents' or guardians' rules. In those cases, the emancipation will most likely be denied and the minor will be sent back home with the parent or guardian.I strongly suspect this is the core of your argument and this is going to be the outcome of your petition.
http://en.wikipedia.org/wiki/Emancipation_of_minorsYour last sentence said your transition wouldn't affect your school work and you're on track to go to college. Understand that if you are emancipated you have to be financially independent, I'm not sure you can work enough to support yourself AND maintain good grades, let alone stay in school and work enough hours to support yourself. I'm not sure that's going to help your transition. For that matter, just because you're emancipated doesn't mean that a doctor is going to medically supervise your transition. A private practice doctor can refuse to treat any patient, for any reason.
Two years can seem like forever when you're 16. The best thing you can do right now is get an education, I can't stress this enough, and focus on the things you can do towards transition in the mean time. 18 will be here soon enough and two years is plenty of time to plan for a successful transition.
Check out
http://gayteens.about.com/od/transgenderteenissues/a/trans_teens_transition.htm I think this might help you focus on what you can do in the next two years.