We've made sure all weapon bones are facing the right way, which is the main issue. We don't do break off hardpoints because that means at least a week of extra work (We'd have to make over 20 models for the ISD, and 140 for the Executor) for a single ship, which we are NOT doing. As for engine glows, we're using the plane method at least for now because when you use particles, scaling becomes a large issue and EaW's engine particles look like complete shit anyways, so unless we make our own new particles, we're not doing them that way. The particle method requires a new particle for every single ship, sometimes more if the ship has more than one type or size of engine. There're 56 ships in the first release alone, that means at LEAST 56 more particles that would need to be made and put into the mod. Not only does that take a lot of time, but it takes a lot of disk space.
This may seem like small stuff, but in the end it adds weeks, even months to the development time, and we don't have our whole lives for this. The stuff you've mentioned could only be done by one person on the team, and he's already overworked. He's our only animator, he does all the rigging, he does well over half the skins and he does a lot of modeling too. It comes down to whether you'd rather have death clones and infantry that actually move and down just slide, or if you want some engines to shut down when the ship stops moving. The bones facing the right way is obviously important, but the other things are small enough that pretty much nobody will ever even notice them, and they don't effect gameplay at all while still pushing everything back.
As for team colours, most of the units have that.