I think they wanted to focus more on sam and kevin then tron. the father dad relationship. Poor tron was reprogrammed, so he was pretty neutered. His turn was semi sudden, but it was kinda built in when he first made sam bleed. He remembered "Users" and he did semi protect sam by picking him up instead of derezzing like he probably would have with anyone else. Because no one knew he was sam at the time.
and when he seen the creator kevin flynn up close, im sure that had to bring back memories, which is what it did because soon after they played the sound bite of him saying,"flynn go!"
I see what you mean though on how the black guards also look pretty much the same, because they are red and have helmets. the only thing really making tron stand out is his T,dual disc,fighting style. But hes always hanging with clu, unless instructed to do something.