Its not so much you looking at it the wrong way, as it being a moot argument for both parties, because both are coming from different positions. There's no reason you shouldn't be happy with what Deus Ex offered, but you probably wont be able to fully understand what others are requesting, or more specifically why, because they're coming from a different outlook.
Ultimately it boils down to the role playing experience Deus Ex tried to accomplish, and that is giving the player a set of tools and customisable abilities, but never allowing them to max out everything. You, the player, would 'build' a style of character that suited how you wanted to play, and levels would be designed in a way that allowed you to integrate your playstyle in a successful way. You could never hack a single terminal and still get through the game quite fine. It wasn't so much about advantages or disadvantages, as difference.
Deus Ex: Human Revolution is excellent, but its praxis, XP and aug distribution counters this old design by having the player max out many important augs early on, while the level design puts a pretty strong emphasis on hacking. There's not enough balance between the offered playstyles, with too greater reward for playing a very, very specific build against playing another.
What most are asking is for a bit more balance to the builds. Whether they should accomplish that through XP and Praxis distribution, the augs themselves, or the level design is another matter entirely.