Regarding the 3D, it depends on what you're comparing it to. Compared to other 3D games at the time, EMI was one of the better looking ones. But compared to 2D games of the same period, it was ugly. The tech just wasn't there yet to make a 3D game that could compete with a 2D game visually, but there was apparently market pressure to use 3D models in every new game. Even at the time, I didn't like this trend -- yes, developers have to use new technology to make it better, but it resulted in a lot of very crude-looking games.
Probably the games that looked the best at the time and have aged the best are the more stylized ones. I think Grim Fandango is a good example of this -- the models look like they were designed to be simple, rather than looking like a poor approximation of something else. EMI doesn't have that going for it, so the look of it doesn't hold up as well, in my opinion.