It mainly effects the narrative aspect, that's correct. But that's not only AP doing it so . If you neglect the fact, that levels in the original Deus Ex have been much bigger than in AP, it's also a railroaded storyline where the final decision about the ending sequence is made during the last mission. Saved the game and played all three endings one after another. What you have done before has absolutely no influence on the game.
Now, many look at Deus Ex as a great game. The illusion of C&C is mainly made by large levels and different approaches (sneak, tech, fire) to solve the mission. Yes, you can let your brother die, you can kill Anna Navarre, but with no further consequences besides some dialog changes. It only affects your own reception. That's the same freedom of choice you also have in AP, 'though AP's level design is really straight forward and you always have the impression of being put into a corset. But that's a personal impression, you can barely backup with neutral arguments.
Risen has a different approach to RP and meets the expectations of exploring a world and developing your character based on a system of skills and talent. For that, it offers more freedom of choice than AP. But I never had the feeling, Obsidian tried to compete with that. It's an interesting story, those narration unfolds differently depending on your choices mainly done during dialogs.
I finished it a second time just some weeks ago, after a long time it had spend on the shelf. I was a little bit disappointed after my first walkthrough. I thought of the story being a little bit confusing, I also expected a little more from the gameplay. But the second time I saw the difference how it plays out in the end. For example, during the first I was not able to convince Parker, because I didn't have the dossier. I underestimated that aspect of the game and also missed many possibilities to gain access to that files. So in several missions I didn't have the information needed to get more options. Yes, it's simply a difference in dialogs, but during the second walkthrough the story became much clearer. I played another kind of character, chose different allies and got different insights, as depending on your allies the understanding of the circumstances varies.
It's another approach to RP and for sure something you can dispute endlessly if you prefer it that way or the other. For me, it was fine. It's sad that Sega canned the franchise. There have been some interesting side aspects that never got fully answered and indicated a possible sequel.