I don't even know why I'm bothering on a two month old comment full of "it's science I follow truth and absolute objectivity~" peppered with "fuck you!!" expletives (much science. so objectivity. wow.), but:

If, for example, after a lot of research we see that people who are MTF for example seem to have a 'female brain' that would lead me to conclude it is NOT a mental illness.

If we instead see that, for example, MTF have a 'male brain' BUT we can see some feminized characteristics that would lead to possible conclusion of a mental illness.

You do realize that the leading research supports both of these claims at once, correct? Trans men, before hormones, have brains structurally identical to cis men. Trans women have "feminized" brains. So what, trans women are mentally ill but trans men are not in this model? This makes no sense and literally topples your entire theory.

My fear is that IF (IF as I have no idea) being transgender does fall into the category of a mental illness that what we have is a problem where we are not only allowing but ENCOURAGING young children to 'embrace their feelings'.

Pretty much the entire scientific community and the mental health community agree that it's beneficial for trans people to embrace those feelings. It's considered a form of reparative therapy to try and "de-trans" someone, because it doesn't work.

We are just beginning to understand the mystery of synaptic pruning, neuroplasticity and general brain development.

I dunno man, you already sound like you've made up your own mind to be honest. I see this a lot, "it's science sorry I don't make the rules" when in reality it's cherry-picking of the highest order used to supplement your findings. Essentially, the same thing you're accusing trans people of doing, you do yourself.