According to this article,
Disney will acquire following movie franchises from Fox.
Fantastic Four movies
Star Wars (the rights to the original and prequel trilogies)
Planet of the Apes series
It will also acquire some of the older films.
Night at the Museum films
Home Alone films
Doctor Dolittle films
To know exactly why, one would have to have access to the contracts. (e.g. even though the Kree first appeared in a Fantastic Four comic Marvel was able to use them for Guardians of The Galaxy)
But the reason why Marvel doesn't own the film rights to some of their properties goes back to the 90s.
In 1996 Marvel filed for bankruptcy.
In 1999 Peter Cuneo ...
According to Forbes:
Part of Disney’s acquisition is set to include the purchase of 20th Century Fox Television. This is not the same thing as Disney purchasing the Fox network, which is not part of the deal.
What Disney is potentially buying is every show Fox produces, including The Simpsons, Family Guy, The Gifted, Empire and off-network shows like ...