Keep in mind that throughout the Epsilon Pegasi missions, the Alliance keeps wasting NTF capital ship after NTF capital ship. I mean, the Cato and Hawkwood (or the Conquest, somehow) in the defense of Enif Station, and then the Rapier, Explorer, Maelstrom, Majestic, Refute, and NTD Normandy in other missions--Koth may not simply have had the luxury of carrying a fleet around with him. He had to use his resources sparingly, and sending his entire fleet to a single attack would have just been overboard. He was trapped, outnumbered, and obviously outgunned, and so he decided to go down in a blaze of glory and one final attempt to do some serious damage.
No real need to rewrite the missions. V had it figured out when they made it, and I think we can live with that. There are some glaring bugs, such as the Thutmose arriving instead of the Sopedu, or the Asuras being a Cain instead of a Llith, but they really are minor and don't drastically affect gameplay. Most of these bugfixes would require changing the voiceacting, and, unless you want to hire back the old voiceactors that performed the roles in the first place, I think we can be happy with a couple of bugs.