It has a lot to do with the fact that when he has a stellar year, it's because he has a couple of great feuds. When those feuds take place, the other guy usually helps carry the load. That guy then usually gets ranked above The Undertaker because they generally do more of the wrestling.
The highest he's ever been rated is 2002, when he was ranked #2. Rob Van Dam came in at #1.
He had a classic feud with Eddie Guerrero over the Intercontinental championship. Before that, had a brief feud with The Undertaker and lost the Hardcore title. After that, he ended up beating The Undertaker for the Undisputed Championship on Raw. However, the decision was reversed. Then, to keep things rolling he ended up beating Guerrero for the Intercontinental title in a classic Ladder Match on Raw.
Then, he lost to Brock Lesnar in the finals of the King Of The Ring title, but defended his title twice by DQ with Brock, still holding the gold.
After that, he beat Jeff Hardy in a unification bout for the IC and European titles. Then, finally lost the title to Chris Benoit. Then, he won the title back and unified that title with the Hardcore title in a match with Tommy Dreamer. Essentially, he held three unified title at once at this point.
Then, he lost the IC title to Jericho, when he and Triple H were feuding. Triple H cost him the title. He was about to beat Triple H a few times, but Ric Flair stopped that. So, he ends up beating Ric Flair.
That's a pretty monster year. Consider The Undertaker had the Undisputed title, he'd have a good chance at beating this, so to say. However, would you put it over the year RVD had? I wouldn't. That was a great year for RVD.
Classic matches, a few good feuds and a good hand all over the card. Unified titles and played well in the main event. All on wrestling, as well, as he's not a great talker.
And this is just an example. Every time The Undertaker has a good year, it's just hard to put The Undertaker's year above the guy at #1. Same thing that happened the time The Undertaker came in 5th or 6th or what have you.