Reusing a ride system didn't stop Uni from building Spider-Man and Transformers next door to each other. I think a third incarnation of the same system might be pushing it, but my point is that I'd have no qualms about another EMV attraction at WDW. However (and I know I don't speak for everyone on this), I'd love for it to incorporate 3D like the aforementioned Universal attractions do. I do love Disneyland's Indy, but even if they upped the ante with better and more animatronics, I think there's a dynamic that comes with the 3D on a ride like Transformers that creates a more immersive experience. The sense of speed, movement, and immersion on that type of attraction is really something, and I believe that combining 3D projections with actual physical sets is the current sweet-spot of E-ticket theme park attractions (those two Uni rides, and Ratatouille at DLP, for example).
While I'm not a fan of the Transformers theme, the ride experience itself is pretty amazing. If Disney made an Indy-themed EMV attraction that borrowed some 3D screen tech from Spider-Man/Transformers/Ratatouille, it would be nothing like Dinosaur.
So basically what I'm saying is that reusing a ride conveyance system doesn't necessarily mean the attraction will feel repetitive. The Ratatouille attraction is proof that Disney can do a 3D hybrid attraction the right way. I'm not sure if trackless would be appropriate for an Indy ride, using EMV (or a more advanced 360-EMV like Universal) along with 3D integration could make a really great Indy attraction (or Star Wars attraction for that matter).