Eh...I love Alpha Protocol, but it has far more emphasis on discreet dialogue mechanics and things like that than a skill based setup for progressing through the game. Deus Ex actually didn't give you a ton of choice in terms of altering the story, some things but mostly minor, but it gave you so much choice in going about missions. AP and even HR were pretty good about that, certainly more than most games, but not remotely at the level of DE. I would liken the flexibility afforded the player in DE to being close to something like Fallout 2, where every situation feels like you can organically approach it in virtually any way, where these other games tend to have a more clear 'stealth' 'loud' 'hacking' 'shooting' type dynamic.
I guess what I mean is, DE tended to have lots of moving parts in a level, and you could overcome any individual obstacle any number of ways and be rewarded for it with items, secrets, progress, better vantage, whatever. Typically in other games you're really forced to go all in quiet/loud and it kind of railroads you down that path once you're going that way. The original involved a lot more exploration if you wanted to make the most of your abilities. The main things holding other games back tend to be level design (Primarily this, designing levels that feel so open ended that they don't make everything obvious is tough - DE pulled it off), and also the skill systems. Deus Ex wasn't afraid to make you specialize and be legitimately bad at things that you didn't level up. This made it so even what was POSSIBLE would change from game to game and really put an emphasis on creativity. People tend to dump on Mass Effect 1 for having a Deus Ex style shooting system, but I think that it was a virtue to Deus Ex, since it put all of your various combat skill squarely as a choice vs your others, you had to consciously decide to be worth a damn with a sniper rifle, and if you did you made damn sure you went paths that let you utilize it, all the newer games make it too easy to be 'good enough' at literally everything, and often an expert at everything by the end. This is the single worst part of HR imo.
