Are there any unexplained branches of evolution?

The origins of bats are very poorly documented by fossils, as I understand it. That shouldn't be too surprising if the ancestors were small, light-boned forest dwellers. There are bunches of invertebrates with almost no fossil record, too, but I'm trying to figure out where I read about examples. (The memory is the second thing to go.....)

A Google on "whale" with each of the names "Thewissen" and "Gingerich" will correct your recollection. Both Pakicetus and Ambulocetus are at least 50% complete, with pelvisis, legs, skulls, etc. Not "pieces here and there." Heck, National Geographic had an issue a few years back that showed a bunch of the fossils.