When I first saw the new design, I loved it. I missed the colored nacelle caps as others have mentioned. It took me a while to warm up to the black strips on the sides of the nacelles, but I wasn't bothered by the change on the outside. Actually, my first thought was the engines were still under construction and the black parts would have been covered by the time it launched. I even liked the changes in all the sets.
What did bother me was, after building up the new enterprise almost like a character, calling it "her" and "she", the computer now had a very harsh mechanical male voice with this abrasive buzzer. I realize that ships being "female" is just navel tradition, and the computer voice is technically a separate thing. But I think the fact that computer was heard so frequently through the film (always bringing bad news), coupled with the very sterile look of the interior sets, gave me the sense that the new Enterprise was a very cold and dangerous place to be. Unlike the TOS enterprise, where even thought there was danger in space, the Enterprise felt like a home. The new Enterprise felt like a deathtrap. People dying in transporter beams, warp engine imbalance. To me this was NOT the same ship that brought Kirk and crew back home safely after 5 years.
Which, to an extent, I believe was the intent of the film. However it was so much that it lost any connection in my mind with the TOS enterprise. I think had there been more time, much of these would have been ironed out in the sound mixing process. What we got in the DE I think helps a lot with making the computer female again and changing the Red alert to more of a siren (though I wish they just would stay with the classic red alert sound from TOS). But even without changing the sound effect, Star Trek II and III made much more selective use of that TMP red alert klaxon / buzzer (so much so that it almost blends in with the music in III).