One thing to remember, there may be people here who've never played the actual FS1, but rather FSPort. I myself haven't touched the actual FS1 game since 2003, and while a few things for me stand out from playing the original game, I've played the Port far more than I ever played the original. As a result, most of my gameplay memories are from FSPort.
In recent play-throughs of the last mission, I've found that I am best served by going after the fighters. In the previous mission, grab a Hercules with the quad bank of Prom and twin bank of Banshees, then loadout the missile banks entirely with Interceptors. Then full-out burn for the node ignoring everything. Then, when I start the next mission, I focus my attention on all fighters, and go after turrets or the reactors between waves. I also learn the patterns of arriving fighter waves and camp out near the fighter bays and pick them off as they launch. I pretty much leave the reactors to the bombers and the rest is easy... granted "easy" is my difficulty setting.