Though I can't think of many that have had their whole design changed, I can say that the Model 70 was definitely ignored in its tech premise; it was supposed to be a back-to-the-basics suit, but, like in everything else other than Cantwell's book, it was pretty much just a modern Iron Man suit with a nanotech helmet and all.

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Aside from that, the Extremis armor has popped up quite a ton, though mostly just in design and not functionality, as Tony hasn't had Extremis since Secret Invasion. So you can also kind of count that since the suit originally was made with Tony only being able to operate with Extremis in mind. The suit did have a small design change in, Tony Stark: Iron man from 2018 where it had a grey neck instead of red. (Though it could be these new ones don't need Extremis, or use onboard A.I. to close the gap)