It's not the same game for one thing. Music is missing and the game is different, I would not say it is better or not but it is different. I could be wrong but I view mods as something to improve replay value, after you have played the original first.
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Actually I believe that there are ways to get Tutu to use the original music and such. I suppose whether or not you use it depends on what you are playing the game for. It is a slightly different game with Tutu, I agree with you on that, however I would have to say that I am of the opinion that the improvements made to the game for BG2 that you get with Tutu far outweigh the limited experience (not ingame XP mind...) benefits that you get playing un-modded. Just the walk speed alone is worth the mod in my mind! "