The color is definitely better, much more comfortable to the eye.
For the weapons, i don't think it's possible for some ships to mount some faction weapons only. The easy way would be to make them built in but then again, it limit the customization and the fun (laser boats can get quite boring after a while).
The ideal way of fixing the gun problem would be to cover some of those mounts. You can still add medium or small mounts on top of them later if needed. Something like this (just an example).
But even outside of the weapons mounts, there's still quite a few issues. Huge number of launch bays, huge burn-speed, incredible shield-efficiency... Plus the drones, while i like the idea, the AI tends to have troubles with those. Perhaps for only one or two tanking oriented ships? It will have to be dealt with eventually anyway.
The blues, while not as broken, still have a few issues too. But i'm sure you'll find most of the problems yourself now that DR posted his modding guide.