There's no real difference from a rider's perspective. The only differences between the two rides are slight mechanical variations, the elevators on Transformers (which you aren't supposed to notice) and the type of animation on the screens. They're the exact same ride system otherwise. A very particular ride system. It's not like a ride that relies solely on practical sets, which can make for a very different experience. There are sets, but you're staring at screens most of the time. People will definitely notice the similarity. Having them in the same park, in the same land even, would be much worse.
Shrek and Terminator aren't rides, but regardless, I've seen people complain about the amount of 3-D in the park (myself included.) People at Uni have even taken to calling Production Central "Glasses Alley" for that very reason. They're probably more likely to remove Shrek because of it.