What I think was great about an upgrade canister was I viewed it as something money just couldn't buy. It was a priceless and not just a mundane piece of equipment, it was not some mere resources, and, as it had almost no drawback at all, it was really some kind of the ultimate reward.
Of course, we can debate if these kind of ultimate rewards, which cannot be manage by the player, are really that important in a video game like Deus Ex. The only way to be sure would be to try it. But I do know that Invisible War certainly made biomods somewhat more mundane and the result was not that great. I was far less excited about finding a biomods than finding an upgrade canister.
The truth is, for most of us, the only standard that we have is we want games that are not made with the 10 years old kid in mind. Unfortunately, it seems that this simple demand is already too much too ask.