I've played the games and now I've read the graphic novels and I've gotta say I enjoyed both a lot. However, I still prefer the game not just because I don't get to play Kyle Katarn, the most awesome Expanded Universe character I know, but because its like they did some things better in the games. Also, they sort of deflated some of the awesomeness of Kyle Katarn in the books but he still kicked butt.
The main thing I didn't like in the books was that they sort of just ignored the majority of the first Dark Forces game. Its almost as if they didn't even happen. They get the part where Kyle steals the Death Star plans but leave out the whole arc where he destroys the Empires plans for Dark Troopers and became one of the few people who defeated Boba Fett. In fact, the one point where Boba Fett comes up in the books, he acts like he never met or even fought the guy; maybe it was such an embarrassing moment as a Mandalorian (though not as bad as what happened in Return of the Jedi, such a noob way to go).
This leads to my next point that they didn't just skip the game but they ignored its impact on the people in the Star Wars universe. Mon Mothma was suspicious of Kyle before he stole the plans for the Death Star and then less so after that but she still was and they showed that in the book. However, considering how much Imperial butt he kicked in the first Dark Forces game and on her orders, that's pretty rough.
Another thing that was disappointing and I wish they'd have given it more depth was his Imperial Academy training. He leads one strike mission, graduate, finds out about his dad's murder, finds out the Imperials actually did it, and then he defects. The author doesn't let him go on more missions which would have given more experience as a soldier and mercenary and also explain his prowess in the video games as a one man army. It also would have shown him express early on hate and a leaning to the dark side before his force powers came to fruition because he thought the rebellion had killed his dad. But no, he just does one mission, feels angry and then finds the truth and changes his mind. Maybe he wanted to emphasize his growth in the force helping him to become this way more than experience which is fine I guess too, it makes it more awesome that he became a Jedi Knight on his own (with help from a dead Jedi Master though) and in such a short time period. Luke did that too if I'm not mistaken.
Going back to the one man army comment, that is another let down. He acts more like a spy at times and other times like he's trying to conserve ammo for some reason. The one time they kind of show off his awesomeness as a one man army is when he infiltrates the Imperial base for the Death Star plans but that's the end of it. I guess it makes more sense though considering his prowess with the force which continues to grow through the series and most Jedi might go for stealth more than strength but if Knights of the Old Republic said anything about the types of Jedi, it was that some were diplomatic, some were stealthy, and some were soldierly and Kyle is definitely more of the last and first kind, not the second.
I'm also kind of disappointed they didn't bring the live action actors back in the 3rd game for live action scenes but I guess live action scenes in games do tend be low budget and corny often so that's why they just stuck with in game acting for the 3rd game plus they were more necessary in a time when games had bad resolution and live action just looked better. Mind you, the scenes weren't corny and they were pretty serious and had alright acting but the special effects weren't great.
What I did like was the inclusion of more characters, the game seemed kind of microcosmic because there were just a few speaking characters of any importance in the second and first game with a whole lot of faceless mooks. Now you got political refugees on the planet containing the Valley of the Jedi, stormtroopers with friends and family, officers with aspirations, and so forth.
I also liked a lot how they explained the back story of the Valley of the Jedi because they didn't explain it enough in the game. Few thousand years before the game, an army of light side Jedi fought an army of dark side Jedi and they met at a final confrontation where the dark siders made a force bomb called a "thought bomb" and killed everyone. Its a really creepy and crazy attack too and it made Kyle more awesome that he was able to free all the spirits it trapped. Here's a detailed article on it too: http://starwars.wikia.com/wiki/Thought_bomb
Anyways, another cool thing was how he got used the lightsaber so fast, he defeated 7 Jedi Knights so easily, easier than I could in the game mind you. He didn't even need a lightsaber for 2 of them, one he just shot in the face and the other he just beat to death. He also uses smart tactics to defeat them such as how he used the anger of one Dark Jedi to make him lose his concentration and then against the Big Bad, he made a force bubble around the guy to cut off his connection to the power from the Valley of the Jedi; I had to chase him around in the freakin' game hacking away with my light saber and dodging those crazy Force Destruction attacks. On a side note, I wish that attack was more prevalent, its like a Force Hadoken except you don't have to be standing still to use it.
Finally, his relationship with his partner was expanded upon earlier on than in the games too; considering the years they spent together between when they met and the second game, it would only make sense. In the game though, they just didn't emphasize any of it and it was almost like the developers didn't want a relationship between the 2 and then they changed their mind in the 3rd game.
Aside from that, I enjoyed the whole story and action and awesomeness of Kyle Katarn, the Star Wars universe needed more awesome characters like him. Its almost like giving a normal awesome character like Han Solo and giving him Force powers. I might not want them to make a book on the last 2 games though, Jedi Outcast and Jedi Academy, considering they delved a lot in the story already in the game as opposed to not so much in the previous games.