Pouk, I have two more suggestions (that you'll probably turn down) for your consideration:
1) Don't give the Vaygr a Battleship. I know you've said you want to make big ships, so you probably won't take this suggestion, but please read my reasoning before throwing out this idea. The Vaygr are more about lots of small, fast ships than they are about big ships. If the Battlecruiser is their biggest warship, then they have to build more of them to compete with a single Hiigaran Battleship. A Supercarrier is really the best big ship for the Vaygr because it fits their swarming style.
2) Make Modular Destroyer Research an upgrade of the regular Destroyer hull, rather than its own hull design. Once Modular Destroyers are researched, you can still build a regular Destroyer for the same cost as before, but it will actually be a Modular Destoryer outfitted with the same weapons as a regular Destroyer (that can be replaced if needed). Empty Modular Destroyer hulls could still be a build option, as well. This plan allows Modular Destroyers and regular Destroyers to both benefit when armour and engine research for Destroyers is done.
On another note, if you would like any help with writing build tree and reseach tree descriptions, I'd be happy to assist. I've got no modelling or scripting skills, but I'm a pretty good writer.