The lack of vocal harmonies is a big one to me. It makes the songs feel incomplete and raw. Obviously they were going for the raw thrash sound, so that's just personal taste, but that's a big one for me.
The Black Album and Load/Reload have a lot of harmonies for Metallica, and that's why I prefer a lot of those songs over their other material. They feel like developed songwriting, with a strong sense of musicality and melody, and not just grunting out an E (which Hetfield had mastered!)
But I only listen to the GHIII version of the album, so the production is just fine. The album was very well recorded, with good guitar and bass tones, and a nice natural drum sound. Unfortunately what ended up on the final album is unlistenable.