When you're translating something 2D to 3D, it usually is. For something to look "right" in 3D, there's a lot of rules that have to be followed in terms of lighting, animation, how an object is portrayed in 3D space...
These rules don't have to apply to 2D.
It's not so much as being a purist and wanting to see the game in its original format, its a matter of...
Does this game really need to be in 3D? Is there any benefits to it being in 3D? Wasn't the original 2D game functional enough? Sure, it portrayed events in a psuedo-3D space, but it didn't need to be remade in 3D, did it? There was nothing wrong with it in its current format.
In bringing the game to 3D, you introduce a lot of potential problems, in terms of a different art style, how this effects gameplay, collision detection, etc.
I'd be more excited for "Turtles in Time HD Remix" than "Turtles in Time 3D Remix".