Yeah the 3D is always something that's bothered me about EMI. Considering that it's all pre-rendered there really aren't any technological reasons for EMI or GF looking better or worse — it's simply down to the skill and execution of the artists.
The author of the article said otherwise, but IMO Grim Fandango's 3D is way above that of EMI's and looks infinitely more grounded, believable, and generally immersive. It seems with EMI they tried to cartoonify the style too much, resulting in everything just looking chunky and lacking atmosphere. The lightning is also exceedingly bland throughout, not to mention the choice of camera angles.
Then you've got that fact that some of EMI's 3D is just downright poor and clearly done with extreme haste. I mean, look at the pictures below: blurry, lacking detail, and just generally crappy-looking.
Still, like I say I did enjoy the game and my younger self was able to look past these things due to the euphoria of having a new Monkey Island game.
I just wish the pirate theme wasn't so lacking; the takeover thing didn't work that well for me, even though the story was executed quite well. Maybe they just went too far with it, I'm not sure. Just not enough piratey pirates for me.