Hopefully some chad takes this on, as I have no skills in this area to speak of. Basically I feel like biological ships are way higher on a 'technological' level than normal ships. It feels very odd to select them at the start of a game without even having gene-modification so my proposal:

Make Bio-shipset un-selectable at start.

Make an event that follows biogenesis ascension.

This event allows the empire to choose to change shipset (Shell or Spine). Old ships stick around in fleets but all bases and stations are swapped for bio equivalents. All technologies for alloy ships are swapped out for bio-shipset equivalents.

This gives the empire access to the bioships if they desire, and it can be thematic for biogenesis given the species is going through a massive change.

If you are a mega chad you could dream up an origin to get access to bioships immediately (Ie trigger a slightly different event at the start of the game).

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Mostly this is a narrative rich mod, I wouldn't expect this to be overpowered as it arguably might trip up your build up in game. But I feel like its a way to gatekeep bio-ships behind logical progression.

Like I can't imagine a biological species somehow wielding bio-engineering without first using metals. Which requires their tech progression to somewhat mirror normal stellaris progression. Barring of course wilderness that is.