I think the key point of conspiracy theory is the paranoiac feeling that an individual cannot trust any modern organization. Details may vary but it is true that we don't have a simple and clear vision on how the modern complex politics and economy are working (I personally prefer much more subtle approach than DXs did, though). Also, in two games, conspiracy theory works in a different way. In the original, even if the dominant political organizations are treachery, it was clear which is the good guys and which is the villains. In DXIW, there are no such distinctive differences among groups. Although this enhanced the grayness of the world, it also reduced dramatic character interactions (Even J. C. Denton's sunglass was ingenious not because it make him look like a Terminator clone
but because it depends on the players to imagine his expression...subtleness doesn't always mean irresponsibility.) and, as a result, made NPC interactions and character development feel soulless, mechanical and empty. Talking of being soulless, somehow, IW doesn't feel hardboiled, either. In well-written hardboiled novels, the main characters are much more interesting than Alex D can be. The conspiracy theory aspect of Invisible War offered a lot of interesting political satires, which the players cannot interact with like NPCs in Deus EX. Then, why did they release it as a game rather than a Sci-Fi novel? I know the balancing simulation essences and emotional effects is tough but I like to seem more of these games which carry both deeper emotional effects and themes, which makes interactive simulation interesting.
OT
As for the genre argument,
Gamasutra: What's the origin of the name “Junction Point?”
WS: When I was with Looking Glass, the last thing I worked on with them on was a concept that I came up with along with Doug Church and some other guys. It was a very different approach to multiplayer online games called Junction Point. I loved the name and concept. I'm not revealing anything too dramatic since we're not doing the game, though I'd love to some day, but the name spoke to me more as a name for a studio than a name for a game. A junction point is where a lot of things come together and that you can go in a lot of different directions. If you think about the kind of games I like to work on and play, it's a lot of genres coming together. If you look at Deus Ex, we still win best role playing, action and story game awards [even today]. I love the fact that we confound the marketing people, frankly. Junction point expresses that. The games I like to make are all about players choosing directions, paths and play styles. A place where a lot of things come together and offer a lot of places to go... what better name could there be? It's also nice that it abbreviates to JPS, which rolls off the tongue.
From a Gamsutra interview "
All For Games: An Interview with Warren Spector"
Even in movies, we normally don't mix the criticism about works itself with other factors. However, about video games, I often come across arguments among "sects" such as genres, platforms and, quite often, rumors, or, what we are not sure of, about economic relationship between publishers and developers. There are definitely pressures from stakeholders since major games tend to consume much money and many developers complains of the pressure. However, personally, I think the games should be evaluated by their own just like movies and influences from the outside should be treated as secondary information.
That said, at least, considering the current status, investing on video games is a risky business and stakeholders naturally like to reduce the risk. If someone doesn't like it, then, I recommend him/her to look for indies, or games which have less stakeholders. If you like to see more of experimental side of the video games combined with modern technology like myself, find your favorite designers and track them. In this case, though, the designers probably need your support, especially money. Sometimes, you may have to choose lesser "evils." For example, Steam has its own defects but I think it's better than what Microsoft is planning. They try to take even "server maintenance fee." The company seems to have concluded that it is much easier to squeeze money from individual gamers rather than from professional companies. For Microsoft, it is just a natural shift and it explains the huge investment to their console. You will get a "bargain" at first but they are planning further and eventually you are going to pay them more. For this, MS wants their "customers" to stay uneducated. I am not doing Anti-MS propaganda but I cannot but agree with Spector and Levine that both gamers and designers should know better. However, I guess I have derailed too much...