I run my heavier class robots with their batteries in series to up the voltage. These are matching pairs of voltages and capacities so I end up adding in just the one fuse, treating them as a single battery in effect, like you mention for parallel batteries. Do you have a wiring diagram of how this would work? I wouldn't have thought takeoffs in the middle of the series chain would work as you describe but I don't claim to be particularly knowledgable with electrics. Perhaps it is my lack of understanding.

Whilst fusing them individually might make sense, I'd be more worried about exhausting the smaller capacity batteries first. I have that same concern with my batteries in series if I don't get enough time to charge them or change them around. Having a fuse at each stage of the series wouldn't have prevented that I wouldn't have thought?