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I realize one of the differences is that Soul Hackers focuses on story and characters a lot more as well as the demon fusion system from other SMT games.
I am talking more about gameplay mechanics such as non-linearity, replay value, exploring, puzzles, how expansive the dungeons are, side quests, unique items and rewards, which game has more depth in the combat etc.
Soul Hackers. I've played the Japanese version and it's an incredibly good game. Everything from the gameplay to the story and music is great in the game. I've tried the Etrian Odyssey series and can understand the appeal, but personally think it's poorly designed. Since without a guide you don't know how to build your characters and even with builds from guides/advice on forums the game is still ridiculously hard and requires insane amounts of grinding. The fourth supposedly introduces a casual mode that might fix this problem, but I doubt it. Both games are linear. Also, both have bonus dungeons. As far as I know, Soul Hackers has like 2 optional dungeons and the 3DS version adds another optional boss. Soul Hackers probably requires the higher amount of strategy between the two while Etrian Odyssey will require way more grinding to progress in the game. It's unfair to compare both though. Since few people have played Soul Hackers and Etrian Odyssey has had it's three previous entries localized.
Why modern education is failing: http://www.youtube.com/watch?v=rM6c-HY8dck