Beyond that, there were a couple of specific reasons:
1) Cyberpunk wasn't a particularly popular theme at the time, and the early 90s CGI art didn't do the game any favors.
2) Many of the game's mechanics were ahead of its time - facedown play, asymmetrical mechanics, etc., all made the game much more difficult to play out of the box than Magic.
3) While the game mechanics themselves were always solid, certain additional elements weren't - specifically, the lack of limits on copies of any particular card made for some broken strategies. Also, some specific mechanics never quite gelled - faceup but unrezzed cards, bad publicity, and traces never really worked particularly elegantly.
You will note that FFG cleaned up all of these problems with the LCG.