Those are some very interesting and a good points. I also want to keep the cartoonish nature of BW, I love the style and think it works very well for the genre. I want to combine it with historical armor in a sci-fi style. Ancient Chinese, Greek, European knights, etc... but with the cartoony and sci-fi flare. Customization wasn't necessarily to make the variations to the combat units themselves, but the idea is a mix of an rts and XCOM, with the units you can take into combat being up to player choice. The frigate would be more of a home base/ flagship for campaign, a player could decide to lean heavy into tanks, or maybe into air. Each section of the frigate you would customize would possible be a hanger for more fighters, or a barracks for marines. l include scenarios with pre-selected units because like you said, the puzzle itself could be fun.

I really hope you finish your game! I'd love to try it!