I liked the Cataclysm destroyers. "Put the hurt on them."
And that one mission escorting the Republican Taidanii convoy remains the most disturbing thing I think I've ever played. Some stuff has been scarier, but it really got to me that I just couldn't seem to protect the colony ships and kept listening to them die screaming despite my best efforts. I finally ended up withdrawing back to the Kuun-Lan and turning off the volume. When everything finally came for me I just killed it all.
Besides, the the Kuun-Lan is the only one of the motherships that was ever capable of defending itself.