The game that allowed for precise adding of any ship was Grand Fleets. They just changed it to be more like Axis & Allies War at Sea, right as it was getting interesting... the Russo-Japanese war book was coming out.
Well in their defense Grand Fleets III is not out yet - so hard to say if it will be like A&A. They will be using a table of "how many dice do a roll and I need 5's", but other than that I don't think the games will be that similar. I'm sure it is true though that you won't be able to add your own weapons anymore.
While I did like Grand Fleets II, and the cool ship conversion rules, the lack of aircraft was disappointing for me. That's one reason I'm really looking forward to VaS 2.0.
Now given that MG is promising an insane number of ships, one would presume they are using some sort of design forumula to come up with not only ship stats but ship points. I'm sure there will be some tweaking based on playtesting, but given the huge volume of ships I can't imagine each ship would have to be designed without some sort of formulaic approach. Perhaps they will make this public and allow it to be used for "unofficial" ships? Could be handy for a campaign!
Now speaking of VaS 2.0 - how is testing/development going? Can we get any previews or commentary? For one, what's different from Vas 1.0?