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Five Features That Changed Gaming at GamePlanet lists cover systems, moral dilemnas, achievements, co-op and sandbox gameplay as changing the face of gaming. Someone needs to point out sandbox games existed long before GTA3 but in terms of our interest, KotOR, Fable and Fallout 3 all get mentioned:
More information.2) The moral dilemma
I’ll admit I don’t actually know the first game where good or bad choices had to be made by the player but I do remember the first game where it was a major feature and made other developers take notice.
Star Wars: Knights Of the Old Republic is to this day still not only one of the best Star Wars games ever made, but also one of the best role playing games, period. The combat, graphics, settlings, and story - all of this had such incredible polish that it practically made BioWare a household name.
One of the standout features of the title was being able to either follow the "light side" or the "dark side". This was done by having the player make moral decisions. While Knights Of the Old Republic was fairly straightforward with good and evil choices, future games to use this concept would elaborate further. Knights Of the Old Republic 2 had additional grey area in its choices, so the decisions were tougher to make. Mass Effect didn’t even give you the choices between good or evil, as you were always going to be the guy saving the galaxy. Your choices were more confined to playing things by the books, or punching panicking scientists in the face.