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SWTOR had an innovation or two, some more than others:
1) Story detailed environment.
2) The Music was simply hands down amazing. I'd trade in my Darth Malgus doorstop for another disc or 2 on the soundtrack. SWTOR had 6 hours of music in addition to previous KOTOR music.
3) The artwork was brilliant. Any envirornment felt like Star Wars, even if the game wasn't Star Wars'y. When you got close to objects they got clearer (you could read a computer screen if you walked up to it).
4) Added Star Fox! Wouldn't everyone love Star Fox instead of Pokemon? (OK, but gave way to maybe other minigames?)
The rest is left to everyone else to fill in!
What made this game innovative to you?
edit comment: I'm trying to put a positive light on SWTOR.
Want a nice understanding of life? Try Spirit Science: "The Human History"
Recognize the voice? Yep sounds like Penny Arcade's Extra Credits.