When I heard the rumors of a changeover to the Tower, I had a feeling they were true (but for both parks). With Disney's hands slightly tied by Universal Studios (who still holds the rights to use Marvel characters in rides) this left Disney not able to use their 4 billion dollar investment to its fullest. Guardians of the Galaxy is the exception since Universal Studios doesn't hold the rights to that. After the re-skinning of the Maelstrom to Frozen Ever After in EPCOT, and the alteration of Disneyland for Star Wars Land, I believed Disney wouldn't have an issue swapping out any ride. At some point Disney will be able to include Marvel rides and attractions when Universal is no longer able to. Several people have speculated the area where DCA Tower of Terror is located will be entirely re-themed to the Marvel Land space after the Guardians ride installation. I believe this to be true, since adding Guardians to the Tower defeats the theme in that area (the Red Car Trolley and surrounding buildings). This change makes the overall theme of DCA park begin to fall apart yet again. To further the theory, this might be why Disney wouldn't change out Star Tours in Disneyland to a Guardians ride as some people suggested. One lone Marvel ride is not their big picture. As we see with Cars, Toy Story and Star Wars - it's about land sections.
As of now the fate of Florida's Tower ride doesn't appear to be in jeopardy, but since Disney doesn't own The Twilight Zone, I'm afraid that may change one day. The old-Hollywood theme for both DCA and DHS is not going to be necessary once the current refurbishments are complete so the start of big changes can't be denied. The rumor for Florida is that Guardians will find a home somewhere in EPCOT. I'm not against Guardians or Frozen, but I wouldn't be pleased with a Jessica Rabbit theme of some sort in EPCOT for the same reasons, it doesn't make sense there and EPCOT's theme was made as to not include these things. The Frozen animatronics are very impressive, but imagine if that was a ride built from the ground up rather than shoehorned into a space. Unless there is a big change or outcry from customers, I think this trend will continue. Lands of properties will be placed together and an overall theme for a park will not exist.