Both Innoventions and Communicore each had their own strong points
Innoventions brought us Ice Station Cool, the awesome new plaza, and continually updated exhibits.
The main problem with Communicore is that it wasn't ever really updated. The stuff that was there was fun, but it needed to be changed once in a while. At the very least, it needed a technology upgrade.
I prefer Innoventions mainly because it kinda has a Worlds Fair theme. Communicore provided an extension to the other pavilions in Future World, but Innoventions is exposing us to a much wider variety of stuff.
In fact, the only things I really miss from Communicore are the educational stores, Expo Robotics, and the robotic t-shirt painters. Ironically, these all used to be exactly where Ice Station Cool sits today.