I miss 'prototype hull' and 'new class' penalties, and would like to see them come back. I wouldn't want bonuses* for serial production, because now you're altering the established values of things. I don't want to see unlimited 75% Frigates; I'm happy to see three expensive (say 125%, 120%, & 110%) 'class leaders'.
If you don't want to play with penalties, switch them off and everything costs 100%. If you do want them, you pay a little extra for new designs. If we use bonuses, I can't see anyone turning them off and not getting their 'cheap' second dozen ships.
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*The only bonus I'd like is speed. I'd be quite happy if production of a design became faster (but definitely not cheaper) as more were completed.
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Disclaimer: My empire almost always build one yard for each design. I read much fiction on here where empires churn out two dozen freighters, retool their (only) commercial yard, build ten colony ships, retool, seven terraformers, retool, a couple tugs, retool, a dozen new-tech freighters, retool, etc. They end up spending more on retooling than I do on building multiple custom yards. Now that C# Aurora has ditched the per-yard overhead, it will be even more beneficial.
I build a one-slip terraformer yard and leave it producing one ship every forty-four weeks for decades, occasionaly retooling to an upgraded-tech terraformer design. Meanwhile, the yard next door is producing one fuel harvester every thirty-five weeks. The freighter yard has four slips, and the colony transport yard, two. Having six yards with one slip each that retool much less often is going to beat having one yard with 12 slips that retools every time it finishes a 'flight' of ships.