The way the TV shows rip apart the game flow was a big problem for a lot of people.
It also has some of the worst logs and emails you will ever find in a game. Meaning, if you are the type of person who needs to read everything, there are emails that will bog you down for 15 minutes, and a plethora of things to read in every room. If you try to follow all that, half the playtime is reading, and that is not an exaggeration. It's brutal with its side lore.
Some of the later story stuff and bosses are also all over the place. It's at its best early when there is some mystery to it.
You will notice some problems like enemy AI starting to annoy you later on too.
But generally, I agree that it has a really cool and ambitious story and there are some cool-as-hell scenarios. It's fun just to witness everything that's going on.