While I personally enjoy modeled thrusters, not every ship around uses them and doing the work to add them would be a PITA. I say fix the code so that animations actually work for those ships that currently do not have modeled thrusters. Who knows, it might bring out some positives of using bitmap thruster glows in addition to modeled thrusters?
I suppose this discussion also has some bearing on my work with revamping modeled thrusters such as allowing the use of multiple textures(of which the only gotcha is having to move the anims from data\effects to data\maps, I need to figure that out), allowing them to use replacement textures to declare afterburn anims, and working on a guide to making good thruster geometry.