the biggest problem with fps is probably going to be character models and the collision there of. pof specs are somewhat limited with the length of object chains you can use, also limitations with the bounding boxes and the way the game uses them. parent bounding boxes would need to contain all tier own geometry and the geometry of children. the result is larger than necessary radiuses and bounding boxes resulting in more collision tests per object, slowing the system down.
might be faster to radius test each subobject independently and if that check passes, then transform the projectile into each subobject's local space for the bounding box test and tree traversal. of course this requires more transforms. since its more efficient (for collision detection) to keep radiuses and bounding boxes as small as possible to avoid unnecessary tests, it is better to keep the geometric center as close to the actual center of the object (probibly requiring each independent subobject to have a 4x4 transform matrix) to allow for the smallest possible radius and bounding box.
you would then need to have at least an independent rotation center at most a complete skeletal system. every time an object moves about its joint, new transform for the subobject is calculated and children inherit the transform of their parents. then when something hits a subobject you have enough data to transform the colliding object into the colidee's space for bounding box and collision tree tests. important thing is you dont test every single subobject, merely the ones that are most likely to collide.
seems like a lot more math, but considering that there would be very few things such character models would need to be collide tested with, small weapons, the current room geometry or any other objects that are in the way (ships), it becomes faster. of course most of this is overkill if you dont mind an antique looking fps engine. something about on par with quake 2/3 would be adequate since it wouldnt be used primarily as an fps game. i could probably do something at about a quake 1 level with lua, if you dont mind that level of lameness.
i sorta wrote a doom-esque floorplan system in lua to confine the movement of a player to a planar object, however this system is currently external to freespace. you would need to model rooms of a ship in the same manor as cockpit models then kinda make a 2d map of all walkable areas so you wouldnt need to actually test collide against the ship geometry for general walking around. the test of the system is available
here in 2d form. every 2d object is assumed to be at a uniform elevation, but you can use groups of them to create stairs and ramps and whatnot. you can also do under/overlaping so you can create bridges and multiple levels (unlike doom). its still kinda quirky but i bet it will work better/faster in freespace.