When you change the colour of a texture you change more than just the colour, you change the effect of certain light spectrums on it, you bring details that sometimes are often left wihtout emphasis, or conversey you hide details that are normally present.
Looking at it already you can see that it appears brighter. You make more of the finer points of it, its not pleasant to the eye. Compounding the issue is that you haven't matched the texture mapping style used on previous Liberty ships. It doesn't integrate seamlessly.
The texture scaling makes it feel like it should be fighter sized, especially the ventral engine pod. It needs a complete overhaul to be honest.
from the general post, i agree with turkish. the texture is not in the least doing the model the justice it deserves. instead of manipulating vanilla textures, why not just use the vanilla textures themselves? not only would it fit with the whole liberty line thus, it also helps with optimization, one of the key things igiss strives to keep with this mod. this is why alot of the models AoM and doom, and even jinx made were reworked with vanilla textures, yet you keep manipulating decent textures to create new ones that do not really flaunt the model's awesomeness.
the texture, from the pictures in the OP, are way too bright, and thus make it seem rather flat, the model. you should perhaps get and use 3ds max for texturing if metaseq is limited to what you wish to do? (yuri taught me how to texture in 2 hours in 3ds from scratch, so im definitely sure its not as hard as people make it out to be. if need be i can help you too, obviously).
you know as well as i do, most of the time the general population of the community is happy with whatever modellers are able to conjure up, and that doesnt really help us improve/fix/edit our models to make them better (dont get me wrong guys, you do make some awesome/well placed suggestions, but most of the time, many of you just are happy to post "ZOMG DATS AWESOME, PUT IT INGAME NAU!" and thats not the type of criticism/help modellers look for at times:()
EDIT: oh and, the model is superb, except for one thing. the engine tube part seems to be thinner in comparison to the rest of the body. perhaps beef up the diameter a tad?