Much better layout wise imo. I'm not 100% sure about that pod mind you. It's in the right place but the dish looks undersized as does the pod itself. I think you should lengthen the rear of it slightly so it covers more of the strut because it looks a tad fragile where it is.
The shuttle bay looks just right though, a really nice touch and a good shape! You might be able to get away with raising it just enough to bring the impulse engines inwards slightly. Heck, maybe you could integrate it into the deflector pod to save you lengthening that pod??
The rim of the saucer looks a tad primitive though. Spend a few more polygons to smooth it perhaps?
The textures are rather cartoonish to boot. Windows are oversized I think. Plus the whole ship looks really dirty and low res.
The saucer registry doesn't look right either. I can't put my finger on it but something just isn't quite right there.
Amazing progress though I must say. With a bit of work I'd quite like to give her a spin or three
