The Tekagi mission was hardest because I happened to be in a Crusader at the time, and the damn ships always seemed to get my thruster at one point or the other. Word to the wise, never fly a Crusader against Dragon Fighters if you don't have a thruster. It's bad...just plain bad.
Other than that, the final mission can be a bit difficult, having to shoot up the generators while the sperm fighters swarm around you. I used a method similar to one I used in the Freespace series -- Using the generator's size to my advantage. By hiding in the crevices, I managed to survive until the cutscene rolled... and that ending was just too horrible. the game was building up and you finally open this gate and they all just get sucked in, for no apparant reason. You have just opened the gates to the entire universe, and yet it uses the gate in some
deus ex machina style in that A) the Nomads are gone (even though they aren't
those infected are clean (I can just imagine Order troops running around with vacuum cleaners and slug repellant) and C) Despite the massive battles, the entire galaxy is now at peace and you're a hero. Hoo-ray, how...boring... You'd think maybe they'd let you see some massive fleet battle, you know, with Rhineland ships (many) fighting against swarms of fighters and cruisers, with you in the middle of it as battleship after battleship collapses in a burst of flame......ooh, that was off topic.