It's partially — a small part — an RPG.
The Gothic games (I'm not a fan of those either) at least had you become a nameless almost faceless hero you could put your thoughts on to. Deus Ex makes you into one particular guy with silly facial hair, foppish clothes and a terrible voice that sounds like someone doing a Clint Eastwood impression. In Gothic, you could sort of put yourself into the place of the hero. Hell, at least you could put on different clothes. But these games also have twitch controls that depend on the action skills of the guy behind the keyboard.
I never played the original Fallout games. But Fallout 3 and New Vegas allows customization, a choice of sexes, etc. You don't have to be a weird Canadian ninja. And in the ones I played, you had a pause option and VATS which to me plays out much more like an RPG than a shooter… VATS played out according to skills and ability scores, perks, etc.
The only character progression in Deus Ex is to unlock abilities. Once unlocked, it is STILL up to the guy behind the controller to accomplish based on his twitch-skill with an FPS.
I have issues with the Witcher (first one, I have not played the second one) as an RPG as well. To me it's more of a story action game. Closer to an RPG to me than DEx in that abilities had more to do with game play than timing your moves, aiming etc., like an FPS.
The stealth in DEx requires twitch moving as well. There's no pause, or choosing of abilities in pause mode. Everything is real time. If you move a little out of cover when a guard happens to be looking you are caught. Because of the character? No, because of the controller handling skills of the player.
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My comments on the writing, faces, etc., are a separate issue from it being an RPG. They apply to my other claim, that it is over rated.
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To add to this:
As a general rule, to me, an RPG allows the player some time to think and direct a character or characters. A pause option, or a menu of skills that can come up even in the heat of battle. Directing a character, through level or ability progression, as well as directing him/her through choices, combat, etc., is different than what happens in DEx.
In DEx, you inhabit the actual skin of the character in real time. You run, move and shoot in real time… in first person even. Even avoiding security cameras has nothing to do with your stealth skill… it's a matter of timing for the guy with the controller. This makes it an action game to me, and sets it apart form an RPG.