Surely you can see how refering to the concept behind a game is problematic if I didn't agree with you about what that concept was. We'd have to find some way of figuring out which one of us was right about in our interpretation of what the concept behind Deus Ex was. Without having some abstract definition of the what a concept behind something really is, that would be neigh impossible.
Regardless, you've now expressed how you feel without reference to that nebulous term. Please don't reintroduce it unless you can explain to me why it's relevant =P
Regarding your specific point of "well, IW comes after Deus Ex, had much of the same team working on it, and was build around the same ideas, so clearly, IW has a design further evolved and thus supperior to that of Deus Ex in terms of what the team wanted to accomplish with it", I have a ton of conjecture, speculation and analysis about that to throw at you:
Clearly, the developers didn't think they worked to reinforce the central idea of Deus Ex which was character choice / development
I absolutely agree with you in this quote. The developers thought they worked to reinforce what was good about Deus Ex in Invisible War. Now look, Invisible War's success or lack there of can't really be attributed to this decision; they developed primarily for another platform than PC, one with massive memory constraints, and they used what turned out to be a relatively lousy game engine. Add to that, they had some massive clusterfucks happen during development; for instance, they scrapped all the AI code during crunch because the guy who made it left and the changes they were forced to make meant they couldn't use it anymore. Similarly, everything was originally higher definition and higher resolution, but again, scrapped and compressed down during crunch due to horrible performance. The process appears to have been disorganized and had a lot of people coming and going from it. Whatever IW was in the end, it was not what it was meant to be in a lot of ways.
But one thing is clear: They unified Skills and Augs, and they unified ammunition, and they simplified the inventory, all with a specific purpose. They made a significantly shorter game with significantly more branching in the choices they presented us with. They absolutely felt that the overlapping systems of Deus Ex were unnecessary to what they wanted to do; that they added needless complexity, in the sense that the game became harder and more boring to manage, but that the complexity didn't have any (or enough) upside.
Here's the thing: This was an incorrect analysis, and what they ended up with was _further away_ from their goal than Deus Ex was. Harvey Smith was the head game designer on Invisible War, and the game he ultimately had final cut on, at least in terms of overall systems design, simply didn't function as well, in terms of game mechanics, as Deus Ex did. It didn't give anywhere near the sense of choice and freedom Deus Ex did. You were presented with much fewer and much, much less interesting situations. Presumably, his academic, absolutely thorough, absolutely mistaken, analysis of Deus Ex convinced Spector to let him try his hand at putting together a simpler and hopefully better design. I absolutely believe that Spector the game designer and Harvey the game designer had very different methods for putting together designs, and that Spector perhaps did not fully appreciate the complexity of what he himself put together, whereas Harvey probably had a fairly good understand of his own work. Honestly, at the time, I think noone had a very good idea of what Spector put together, or why it worked... But game design can be like that. When put together creatively rather than analytically, it can potentially grow into something incredibly complicated. Harveys design wasn't complicated, it was analytically put together, and it turns out, it just wasn't as good at providing the player with meaningful choice.
Ultimately, the swimming system was one of the less successful designs, but again, with such a different approach to the design process itself, that's no wonder. I don't think Spector or his team was really able to tell why the overlapping swimming systems was a less fruitful piece of design than the overlapping door-breaking systems...perhaps they weren't even able to tell that it _was_ a less fruitful piece of design. But ultimately, that doesn't matter much: Their process resulted in so many great things that noone has to care if they fully appreciated it. The design on IW appears to have been very much brains first: I think harvey understood everything he designed, I think he knew more or less exactly what it did...I just don't think he understood the original Deus Ex design, or that his improved version was actually worse in terms of what he wanted to do.
Here's a very basic example of where Harveys design was significantly worse than the design of Deus Ex: In Deus Ex, if you had a weapon with limited ammunition but high utility(plenty of these), say the sniper rifle, if you ever chose to use it in combat, you'd have less utility from it for breaking into things. Being one of the weapons that chipped up cameras and low-strength doors, but also one of the weapons best at taking down MJ12 commando's, if you chose to use it as your crowbar of choice for getting into things, your options in combat were limited, and if you chose to kill the MJ12 commando's, you'd have a harder time breaking into things. In IW, you could never ever have this interplay. If you carried a sniper rifle and it was the most efficient weapon for taking something out, there's no incentive there to choose another weapon. In other words, the choice has become much less complex because there's no systems overlap. What is absolutely crucial to the sense of choice is the concept of side-effects: If you do something with something to something, it must influence a third (and potentially a fourth) completely unrelated system to be interesting. If you have multiple ways of shooting with something at a specific person for example, then if each of those ways has unique side effects, then your choice is interesting, because your choice is assymetric and the exact results are hard to predict (but possible to ballpark). This is the quintessentially interesting choice to humans, in my oppinion, and it is incredibly pressent in Deus Ex, while being relatively rare in IW by comparison.
Going back to the example, this is precisely the opposite of what they hoped to accomplish: They wanted you to choose whichever weapon you felt like, but they ignored the fact that certain weapons were clearly better at certain tasks. The simplified system, in turn, made only the most optimal weapons viable, which is just like how it is in other shooters. The lack of overlapping systems didn't give the player more choice; it gave him less choice, because the only choice that was left was too simple to be interesting, and therefore wasn't a choice at all.
Anyway, here's the crux of the matter: Harvey, Spector & Co. did not apparently realize that the overlapping systems they'd build for Deus Ex were key to the success of their design, so when they went in with a top-down design (rather than the bottom-up style of design used for Deus Ex, where it occoured naturally), they didn't include this crucial element. When they tried to understand and optimize their design for IW, as a result of optimization and (incomplete) analysis, they ended up removing core functionality because they didn't fully appreciate how and why Deus Ex works.
And that's essentially why I don't think your allusion to IW's design works. I mean...I also don't think that what the designers intended the product to be is anywhere near as important as what would be a better product, and I think cutting the overlapping systems down would make the product inferior compared to balancing them (no matter what the author design intention may have been)...And even if you think that author intentions are important, your assumption appears to have been that the desingers knew exactly what they were doing and didn't make any critical errors or setbacks in their design of IW, an assumption I strongly question. So reject my above speculation and conjecture at your leisure, if you wish, but your case is far from air-tight either.
At the end, I'd argue that few people truly do understand why the design of Deus Ex works, though the person who probably comes closest is one Jonas Wæver, a little known game designer who came much closer to replicating the feel and sense of play and choice of Deus Ex than ISA ever did, when he designed a bizzare mod for the orignal game....I forget what it's called....The Unnamed Mod I think? But of course, this lack of understanding precisely why it works is why it's worthwhile to discuss.
If you truly understand why Deus Ex works, you're probably ahead of both the academic game design circles, the game development industry, and most of game journalism in terms of your insight into how games work.