Whilst Universal do retain the rights to the use of Marvel in Orlando's theme parks, I'm not sure the brand has a long-term future at Universal as the contractual constraints on adding new attractions and upgrading current attractions will be incredibly tight now Disney owns the brand.
That's why, in my opinion, Transformers would be a great attraction to begin the slow phasing out of Marvel from Islands of Adventure.
This WON'T be an IoA addition for a myriad of reasons. First, there's no where it'll thematically fit with IoA. Second, IoA doesn't need the attendance boosting draw that Transformers will be. The Studios park needs a big draw to even out the crowds between the two parks.
As for an area where it could go, I'm thinking it'll take up the plot between Simpsons and MIB that has always been a prime area for expansion, and it will have an entire mini-land devoted to it.
As for parks I would definitely go with Universal Studios Florida for that. IOA is getting enough traffic thanks to the WWOHP and USF is not drawing capacity even when IOA is slammed during the summer months. So a new high tech attraction like Transformers: The Ride would certainly help draw attendance to that park again. I know USF is also getting Despicable Me but that is not an ambiguous enough of an attraction in my opinion that would draw crowds just to see it for time to come.
As much as Twister sounds like a good ride to replace I can't see it location wise being possible. With the addition of RRR and the track of the coaster going through part of the twister building in the New York corner of the park. Now the track doesn't go over the main auditorium/presentation stage of the building. I don't know the if the size of the footprint of that area is large enough without interfering with RRR, that Universal could build up to the height and footprint size they would need for the Transformers ride. Due to the restraint of the RRR coaster I don't see that option as the easiest to pull of.
I do really like the idea of them putting the ride deeper into the park. I don't see Universal taking out the Fear Factor theater for a ride but see them rather putting a new show in there. Plus they use that theater for Bill and Ted's when HHN is in USF and they also every year use it as a venue for that cheer competition they have at USF along with other events. In addition to those, NBC is rebooting the Fear Factor franchise and is actively taping the new episodes (TMZ already reported on an incident that happend while taping). So the show is back up to date (in the sense that it is an active TV Show again) even with keeping the current theme. Either way, having a show there helps with the crowds on busy days, and personally I'd like to see Universal put on a new quality show once again.
There are two locations I can think of that aren't being used currently, by any attractions anyways. First being the Soundstage behind the Monster Cafe and Donkey's Photo Finish (Shrek meet and greet), and the Train from BTTF. The only thing I know that is being used as storage area. Looking at Google Maps and comparing it to Hollywood, it would seem that if the Train was moved and the building rebuilt it looks like it could possibly be big enough.The second location that could work is the area between the MIB building and the Simpsons Building. Currently that is where 2 sprung tent houses for Halloween Horror Nights are located. I'm sure that area could be repurposed to build a Transformers attraction and still keep room to move those Sprung Tents back further on the lot of land in that area.
They could tear down the T2 building, and redo the parking/bus loop of the hard rock hotel and put it there, but rumors are still floating around of an Avatar based 3D attraction coming to that building (and the Na'vi are going to Disney World).
Great minds, etc. etc.