Happy I stumbled upon this one - This is an incredibly well done thread with an excellent analysis.
One point I can relate too - if in a somewhat different way - is the experience you describe in the OP as a child, not in regard to gender, but in regards to physicality.
Initially it was fine - I was a skinny kid and it was very easy to imagine myself in most heroic roles - but puberty had other plans for me... Which created a certain dissonance. None of the fictional characters I related too on the level of personality looked anything like me. Large man in fiction usually range between good hearted but dimwitted to outright bullies. The wisecracking bastard who likes to keep cards up his sleeves and think on his feet is almost always the lean short actomorph (The only real exception I remember to eventually arrive was from what turned into a pretty low quality show - Tyr from Andromeda). Mind you, imagining yourself with a different body type is not quite as extreme as imagining yourself as a different gender, but I think the effect is still the same - you feel less comfortable making that connection.
One related thing I am curious about - directed at Dana but anyone can answer - if you dislike the depiction of the dumb dad, how do you feel about the companion trope,
the wise mom who was always right all along? Do you think that in itself could have an impact?