The version on the NYC '93 boot is kind of a hybrid between the two. It's basically the original version, but with some extra parts and extended instrumental sections added to Parts III, IV, and V that they kept for final version in '95.
As for the song itself, I do like it a lot, as I love the fact that it has that classic Images and Words feel to it, and I do really wish the song had been on I&W. Oh, and Petrucci's solo in part VI is absolutely mind-blowing. However, I do like a lot of the Deep Purple-esqe organ that Derek added in the '95 version. I'm actually a little torn between which keyboardist I like more on this song, since I feel Derek added a lot of feeling and atmosphere to the final version, but I like a lot of Kevin's distinctive little touches, like the twinkly ascending keyboard pattern in the verse of Part II. I also really like the extended opening and ending in the final version, as it brings the whole song full circle musically, which fits in with the lyrical themes of the song itself (being about the cycle of life and all that). I guess perhaps it is for the best that we have the luxury of having two versions of the song to listen to and enjoy and have little debates like this. Although I would like it if they were somehow able to clean up the quality of the Antiquities version (perhaps in a future Ytsejam release (hint, hint)).