Or, a third option, you're reading too much into the "will" and are thinking that they're implying he didn't have the weakness before... I don't really know.
That's the one.
Supes is weak to magic, he has been for a while, I think, it comes up whenever Captain Marvel shows up in a Superman setting (cause they always fight for some reason)
There's a big history behind it. When Captain Marvel debuted, he went bigger than Superman did. By that, I mean "Super WHO now?" He was the first ever comic super hero to get a live-action TV show based after him. DC sued Fawcett Comics over similarities to run them out of business before they bit the dust. When Fawcett went bankrupt, DC bought the rights to Fawcett created characters, including Captain Marvel whom they revived, with Superman on the intro explaining who he was! So, Superman and Captain Marvel evolved to have a sort of Ryu and Ken relationship, and like Ken is infinitely cooler than Ryu, Captain Marvel is infinitely cooler than Superman.
Bruce Timm had been trying to get Captain Marvel in episodes of Superman: The Animated Series since the beginning, but DC wouldn't allow it. Then when Superman "died" in the finale of Justice League: The Animated Series, Captain Marvel was chosen to be the replacement before Lobo was even written into the script to be Superman's replacement until they decided to resurrect him sometime next season, but DC STILL wouldn't let them use Captain Marvel. So, in Justice League: Unlimited, we got ONE episode with Captain Marvel and Superman fighting, YEARS after Superman: The Animated Series was canceled.
Speaking of which, in the episode Clash, Captain Marvel holds Superman and yells "Shazam!" to bring down the lightning bolt, but holds Superman in the way and just keeps yelling "Shazam!" and keeps striking Superman with lightning bolts. Anyone else see something like this being used in a Brutality or special move?