When the X-Men title ceased publication of new material and shifted to reprints of prior stories, a number of the original covers for those stories were replaced with new work by artist Gil Kane, just as was the case in other reprint titles such as Marvel's Greatest Comics, Marvel Triple Action, and Marvel Tales. In all of these cases, the decision was eventually made to return to and reuse the original cover art and simply make alterations or adaptations where needed--which was likely no reflection on Kane's work, since other artists could have been tapped to do new work if Marvel had wanted to continue in that direction. Perhaps it was simply deemed that the original art was still viable enough to pull "double duty" in terms of reselling the story, while keeping in the spirit of re-presenting a classic story in its entirety.
In that sense, Kane's reinterpretations of those covers may have been unsuitable for what was required in a cover image--namely, that the image serve as a clear and dramatic representation of the events of the story within. Rather than provide that kind of all-inclusive image, Kane tended to take a "snapshot" approach, treating the cover image as an actual page from the story--and in doing so, crammed perhaps too much imagery into the space available. And when you're talking about a team book, the end result could be a jumble of action that admittedly showed you that a lot was going on but by the same token was difficult to sort out and make sense of.
In the climax to a late-1966 story in X-Men, where the museum thief known as El Tigre has achieved the power and status of the Mayan god Kukulcán, the X-Men battle a formidable foe at great personal cost; yet in comparing the two covers to the story, featuring both the original as well as Kane's version for the 1972 reprint, only one of them seems to embody the impact of the team's struggle with this enemy.
In Kane's image, it's clear that the X-Men are in a fight where, despite their numbers, they're at a disadvantage; after all, if your enemy is able to drop nearly all of your team in a single stroke, it's pretty clear that Kukulcán's claim of being the reincarnation of a Mayan god isn't an exaggeration. But in the original image, pencilled by Werner Roth (with an assist by Jack Kirby, whose handiwork appears evident in the depiction of Kukulcán), the impression that the X-Men are on the ropes comes through loud and clear, even without their enemy firing a single shot from his amulet. Also, the word "holocaust" is given prominence on both covers, presumably in order to convey the overall effect and outcome of the X-Men's fight--yet which of these covers brings that word to life for you? More than likely, the one with the field of battle going up in flames--with the X-Men apparently out of options and suffering casualties.
As if Kane's cover isn't busy enough, he also stacks the deck with Marvel Girl, who in the story isn't even present during this battle. In addition, the revised cover completely glosses over the unexpected and near-tragic development of the fight--the critical wounding of the Angel by none other than Cyclops himself, as both were closing in on Kukulcán but who obviously failed to account for each other's intent. Roth's cover portrays the battle's most desperate moment without giving too much away, while still maintaining a heightened sense of danger; while the revised image only conveys the most generic picture of Kukulcán's threat to the X-Men.
A look at the original conception for the reprint cover by Marie Severin.