I'm really having a tough time deciding this one. I think I'm mostly torn between the Transportation and Imagination pavilions. While it sucked to lose my favorite ride, Horizons, SPACE does truly carry the EPCOT spirit and directive. Nemo is an awful theme for Future World, but it more or less just amounts to an overlay, and the basic foundational experience of Seas is still there. Once again, it sucked to lose 20K, but the New Fantasyland should make up for that some, and the playground is good so that there's something for little ones. Stitch is really bad, but is kind of an overlay to Alien Encounter, and I don't really expect it to last, anyways. Tiki Room sucks now, but in all likelihood will have a new show in the relative near future. Toad was replaced by a great ride, I'd consider the Energy change to Ellen more offensive than that. I loved Timekeeper, but MILF at least has the potential to be an excellent show. Nemo and Tarzan are both equally excellent shows, and my personal preference is actually towards Nemo. The Sound show, once again, is easily changeable.
I think my answer would have to be Test Track. Imagination has high odds that it will be restored to something more on par with the original. Unfortunately, Test Track will almost certainly be around for a long time. It's not likely that we'll see something that covers the true scope of transportation for a while. That's a big shame, because I could very easily see something done there that would share all of the exciting transportation concepts out there that would truly fascinate the average person and be much more fulfilling than Test Track.