Finally!! Someone else gets it!! All of those subtleties were lost on the mainstream audience, I think...
They were certainly lost on me. I had no experience with the original franchise other than knowing Captain Sheridan was in it.
I don't think the first movie really had a lot of subtext. In plot/narrative terms it was more of a fantasy adventure film. Indeed just the surface text of the film was often pretty obscure, so you'd need a JCB to uncover and real subtext. It had a lot of interesting ideas mixed with a lot of the old tried and true tropes, but IMO it never fully came together.
Not that I have a problem with the original film you understand. It was a ground breaking and often tragically overlooked piece of art. However, as a film it fails to gave any of it's characters any real depth. Even Flynn is essentially two dimension and practically (and sometimes literally) stumbles through the events that unfold around him. Tron is the only one with any drive but his motivations are essentially just blind faith in his User.
One of the oddest things for me is how awkward and half hearted the quasi-romance jealously triangle (pentagon?) was between Flynn, Baines & Alan/Flynn, Yori & Tron. It felt like it was just there because they had to tick that box, but had no clue what to do with it. As a result Baines is little more than a plot device and Yori is barely more than set decoration.
Something I really appreciated about Legacy is how they addressed this in their handling of Quorra. On the surface she may seem like a typical action-girl/love interest for the male protagonist, but if you actually pay attention you'll note that there is no romance between Sam & Quorra.
There's certainly a connection and a fast friendship but they never reduced her to a damsel in distress or prize to be won. Indeed, she saves or moves to Sam's defence on no less than four occasions, even willingly sacrificing herself at one point so the Flynns can escape. By contrast, Sam comes to her rescue *once*. From a a character arc perspective, this is as much her movie as it is his.
What a lot of people missed is that thematically, they're not a romantic couple but siblings.
This all pretty well illustrates how the whole film was constructed to function on the surface as an action heavy popcorn movie for the masses, while still having a surprising amount of depth for those willing to go looking for it.