The neck on the EVH is an exact digital reproduction of the neck on Ed's red and white striped 5150 guitar of the 80's. The Axis neck is about the same but a little wider at the base so it does feel a little different. There are on going debates on this board as to how different they actually are. The specs are slightly different though.
Other differences are: pickup switch in a different location, rear pot cavity route is much larger on the Axis, Axis has a rear body contour. Plus the Sport models did not come around until Ed left the company.
None of these are necessarily improvements or make the guitar any worse. The fact that there are some differences and the fact that there were only about 6,000 EVH's made means they have a certain collectable value.
As with anything collectable, one man's garbage is another man's gold. If it isn't worth it to you, then you shouldn't buy it. Period. I got my EVH new in '93. So techncally, I'm glad they're worth more.