A few things, like Han shooting first, are cooler in the originals. Also, they totally f***ed up the sabers in the DVD versions. We see Vader with a pink saber at various points, and even though these new blades are supposed to be more liek the prequel sabers, they are frequently assymmetric (the blade doesn't line up w/ the glow). Last, of course, is the inclusion of Hayden Christianson at the end of ROTJ, a decision which does not make sense in terms of the story. Furthermore, Hayden doesn't deserve to be in one of the better movies.
I believe these are the primary gripes, and they are perhaps the only things I would like changed about the DVD version.