I'd happily put it up there with Akira, Snow Crash and the videogame WipEout as the joint most influential pieces of science fiction of the 1990's.
As a movie it captures its era in amber, from the popularity and maturity of videogames to the internet starting to envelop society. The 'goth' elements only serve as a useful visual metaphor for casual audiences as to how teens/YA of the day saw themselves online, a counter-culture operating in a space free of the older generations.
I can see the trans allegory, not in any physical way but rather the characters adopting their internet forum aliases upon exiting the matrix and being able to define their identity on their own terms. Perhaps this is something we all craved?
What the 'red pills' don't seem to realise is that the powers they worship control the media and in turn how they perceive things. They've not been set free as much as been set up with the ultimate tragic manipulation for somebody else's ends.