It was definitely an artistic choice to go with the "retro" visuals. However at the same time, it's like 1 guy or so making these games. I think with a 3D engine, the simplicity of the game would have been lost.
I do get what you mean though, I find some of the difficulty of the game is seeing what is going on. But I think it's as much due to the hectic frantic pace as the visuals.