There's a graphic novel titled "Tron: Betrayal" that helps bridge the gap between the two films. I read it before I saw Tron Legacy; I think it helped me enjoy the movie a lot more.
The graphic novel goes into more depth about Flynn being split between his responsibilities in the real world and in the computer world, his creation of Clu to help him achieve a perfect society in the computer world, and Clu's frustration at Flynn's increasing absence. Eventually Clu decides to take a more active role in realizing the perfection he believes Flynn wants. This makes him more of a sympathetic villain; instead of just being a generic "bad guy", he is genuinely trying to do what he sees as right and he resents Flynn for having a problem with it.
The graphic novel also goes into more of an explanation of the "Isos". In the novel they're interesting; I felt disappointed that the movie does away with them quickly and plays the whole "last of your kind" card.
Ten bucks from Amazon: http://www.amazon.com/Tron-Betrayal-Jai-Nitz/dp/142313463X