i mean something were you can actually fly cap ships in mission
This already possible, just add the "player ship" flag and voila, you can fly a capship.
But there are problems.
You can't control your turrets directly for instance, you'd have to script the entire mission via SEXPs, which isn't the best thing.
Option two would be to change the class of a ship from destroyer to Bomber, means you could control all firepoints, but the turrets otoh have to be controlled via SEXP.
It also means to edit the models in PCS2 since capships don't have firepoints ( means primary and secondary banks ), only turrets.
Nuke has made a script that allows the player to control one turret but if you want to fly a Omega class destroyer or a Sharlin this wouldn't work.
It would require a lot of scripting and/ or coding to make cap ships really controlable by the player.