I ended up voting for Time because it's the version I played out of Time/Darkness. Blue Rescue Team was pretty damn good (totally epic plot, especially the second half), but Explorers of Time took the PMD concept, fleshed it out more, and continued the tradition of having an awesome plot and music. Primal Dialga's battle music is easily one of the best tunes I've ever heard come out of the Pokemon franchise.
I did buy Explorers of the Sky, but I ended putting it down very early on. The additions were fun but handled in a very awkward way.