In my opinion, the changes must remain minimal, and the bugfixing must be done, a game this old cant have mission design bugs.
From what i remember now:
Bugs:
*General:
-Stealth ist really working on the Pegasus, last time i tried AI launched harpoons and hornets at me.
*A game of tag:
-sometimes the Deimos doest shoot at your marked target, even if its in range and beams facing it.
*Bearbaiting:
-Phoenicia must die or not?
*Their finniest hour:
-The Sobek does not unlock beams when you re play it as a mission on the tech room, it does in campaign mode.
*COT2
-No fail debrief
*Apocalypse:
-No cutscenes
-No supernova
-Lemnos sending a msg as "command" even if its dead.
Changes that must be consider at my estimation:
*Bearbaiting:
-Thebes must be a Typhoon, all reinforcement wings arriving at this point must come out of the Thebes fighterbay. And the Thebes must be positioned where the Demon can shoot it with 2 LREDs.
*Their Finniest Hour:
-Adjust Sobek position so it can fire its beam at the cruisers
-Beam free the Aeolus as the Lilith enters the battle. As the Lilith enters it gets in a head-on battle with the Aeolus, its stupid for the Aeolus to not fire back.
-The Colossus is disabled because if its moving it may destroy the Sath, as it happen some times in multi in PXO era. But just remove the disabled thing and put him to stay still, the disabled thing its confusing. Also ill like to see the Colossus to shoot the Sath a few times before dies, even if out of range.
-Adjust Colossus/Command dialog, i can never hear the whole dialog before the Colossus dying off.
*Apocalypse:
-Add more bombers wings, the player may run out of enemy's at the end, that shouldn't be happening, in the video the Shivans are fighting to the end.
Mayor Changes:
-Add more allied ships to "Apocalypse" mainly because there should be more ships at the end that could reach the node, and with more bombers wings attacking them, so the player may decide about jumping out or fight to the end "so others may reach the node".