Well, instead of having a basic cockpit of squares, you could do something where there's strange intertwining lines of the green glass that bunch together near where the cockpit would be, and sort of curve around the ship a bit.
Like I mentioned before, look at almost any sci-fi genre... many alien ships use similar technology to humans in them. Find me an 'alien' window design and I'll gladly use it, but trying to come up with something with no real starting point isnt easy.
I thought about using the round gallic windows, but those are some difficult textures to work with, and look even more human than these do.
EDIT:
As far as details along the neck, I dont really like the look of the extra turret hardpoints there, just seems like they're really bulky on a smallish structure. Here's two different versions, one uses the same glowing stripe the front of the ship has, while the other adds windows along the neck:
I think I like the windowed version better.
Hm... perhaps I should put a glow behind the grates on the front portions of the engines/wings...
Went with the windowed neck, and added armor plates to the top. Also moved the escape pod structure backward so that it connects at the neck of the ship and extends forward:
I'm liking it a fair bit now, but one think I'm curious about. I'd agree the neck turrets don't work, but how would it look with 2 moved onto the wings and 2 moved onto the main hull, leaving 2 centre two where they are now.