Looking absolutely fantastic! My only bit of feedback is that if you intend to scale it up to that size, the windows on the upper structure should be made smaller, right now they're several hundred meters wide. I'd suggest removing them perhaps and replacing them with a number of modules similar to the ISD's bridge with a lot of smaller windows.
Actually I always figured those depressions would merely be dotted with small windows and maybe some greebling, not be hundreds of meters wide windows themselves.
As for the latest version where they're gone... well, it's up to you two to decide, but I find the new general shape of the top dome to be less aesthetically pleasing than the old one, due to the hamburger style. Of course, I only got one screenshot and one angle to look at, and I suppose it does somewhat counterbalance the squashed horizontal profile the old one has.
Also, I'm hoping you could do something to make those big triangular vertical paddles under the main platforms a bit more exciting. Adding the capship docking tubes to them and making them smaller is a good start, but I think they still need something more. Maybe small hangars capable of holding a single fighter, some other kind of large-ish extra features to make them look like they actually have a purpose, some greebling or antennas at the lowest tips and/or some beams between them to connect them, just to give some ideas.
In any case, it's absolutely great that you're tackling this.
One of the bigger lacks right now is how the only station we got is such a crude WIP.
