There's a couple of key things that impact story in games:
1 - Focus. The focus of almost all videogames is the gameplay, not the story. It is almost always a secondary consideration.
2 - Role - The role of a story in most videogames is to provide a framework for the gameplay. Most stories are therefore highly derivative of other mediums that seek to redefine story delivery and concepts.
3 - Talent - The truth is that in most cases videogame stories are being written by low level talent. If you're a serious writer wanting to set the world on fire, you're not thinking about wirting for videogames. This has been improving but it must be recognized the top talent in writing is focused on other mediums
4 - Pacing and Delivery - Narrative and story pacing is different from videgame mechanic pacing and it is tricky to balance the two. Consider that in a videogame there is a need for a lot of gameplay that is mostly superflous to story. Consider Lord of the Rings across three mediums. In the book, the Battle of the Pelnor fields covers maybe 3 to 5pages of actual combat (from my memory anyway out of over 1,000). The focus is on the characters and before/after with a little bit about what happens during the battle. In the film, which is visual and arguably closer to videogame format than book, the battle is expanded enourmously and takes up a lot of screen time, with the character elements reduced around it. In the videogame, the battle would be like 95% of the title with some simple cutscenes.
Now with more money, bigger sales, etc. things are improving, but even so consider sales of essentially non-story driven games vs story driven. The focus is more on getting your multiplayer balanced or sorting our your skill tree than story, pacing, dialogue, character development, etc.
Part of the reason Uncharted 2 was hailed as such a pinacle, often outside of the gaming reporting spehre and in mainstream newspapers, etc. is because it probably does represent a high point of a developer finding a much better balance between gameplay/story pacing, working out how to mix narrative during gameplay and develop characters, and giving enough attention to dialogue and voice delivery.
A good example for me from Uncharted 2 is when you have to carry Jeff and fight. At the same time, ND used that sequence to:
1 - deliver great gameplay and make you enjoy the dramatic moment interactively as the hero
2 - vary the gameplay - instead of constant, fairly repetitive gunplay a'la a lot of FPS suddenly I only have one gun and I have to deal with a slow burden.
3 - expand Nathan's character. It matters to him to try and save Jeff.
4 - expand on Elena and Cloe's character. Cloe thinking of herself, Elena aligned to Nathan. Cloe seeing Nathan's acts as a sign of weakness and lack of commitment to her, Elena the opposite
5 - make you care about getting Jeff to safety and allowing you, during actual gameplay, to evaluate Elena and Cloe's different characters and realise who is better suited to Nathan really and the more natural partner for him.
6 - continue the story in a flowing manner. This sequence flows naturally from the previous sequence and serves as a great way to mix all the above goals
Then, when the next cutscene kicks in, well, most people should care a lot about what happens and have their views on certain characters firmly underscored.
Now, very, very few games in my experience get remotely close to that level of execution between story/gameplay.
Uncharted 2 is a B movie, but as a videogame ND showed more understanding and control of mixing the two mediums than many videogames that clearly had loftier aspirations - for example Heavy Rain, while at times even better, also messed up its story plenty of times as well.
For things to improve we're going to need to see better talent - either attracted to the medium or developing from within it or a mix of the two - and developers deciding up front that story is important and has to be integrated to Uncharted 2 levels rather than serve as a framework that progressing in jumps and starts between cutscenes that deliver a tiny bit if simplistic narrative.