One of the most important things in BOE mission is having everything organized... you see, every ship should have a role on the mission like Caps kill caps, bombers help caps to kill the other caps, and fighters protect or destroy bombers... of course, this is said in a very general way, but you catch my drift.
Also, the big slow prob in FS is not the models... its the textures... take starlancer for example... in my old 800 Mhz with an ATI Rage 2, the last mission of Starlancer, wich had a lot of caps and fighters, runed just fine and smoothely... in FS2's mission where the colossus jumps to kill the repulse for example, the game goes slower with my 1500 Mhz with a Geforce 2!!! And that's just two caps!! Interesting, no??? What I say about being slow is: get rid of Lod's (of course... not debris), and make the ships only change textures to less detailed ones when they get far...