From some cursory research, it seems Disney has been trying to find loopholes around this contract. While Disney can't force Universal to close any attractions, Disney can apparently block Universal from adding any. There's also some weird provision where Marvel characters can only appear in theme parks east of the Mississippi River. So Disneyland can have Marvel characters galavanting around, but Disney World can't. The exclusivity rights for attractions are also only exclusive in the United States so Shanghai Disneyland can have all the Marvel attractions it wants.
I presume as long as Univeral follows the terms of the original contract, it can keep the attractions at Marvel Super Hero Island. I would not be surprised if Disney was watching Universal for any signs of a breach of contract, but Universal holds all the cards. If Disney wanted to toss a bunch of money at Universal to get the themepark rights back, Universal would probably insist on Disney paying to replace/rebrand the Marvel attractions at Universal. Of course, what is popular enough to replace Marvel? Disney would have had a better chance of prying Marvel away before Comcast bought NBCUniversal.
Going back to Nintendo, apparently Universal has a much faster turn around on taking properties and creating theme park attractions. This may be (at least partially) why Nintendo went to Universal over Disney. I'd certainly bet on Nintendo negotiating friendlier terms than Marvel did back in 1994. Nintendo isn't in financial trouble, and its IP are perfect for theme parks. Marvel's contract is apparently forever unless Universal sells back the rights or closes the attractions. Nintendo, being as rightfully cautious as ever, could have negotiated for X-amount of years after opening in order to reevaluate things. Additionally, I'd be absolutely shocked if Nintendo didn't have veto-power on the attractions. For example, if Universal wanted to have Link talk in one of the attractions, Nintendo could tell Universal to sit in the corner and think about what its done.