The Altera Centauri collection has been brought up to date by Darsnan. It comprises every decent scenario he's been able to find anywhere on the web, going back over 20 years.
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Call To Power 2 Cradle 3+ mod in progress: https://apolyton.net/forum/other-games/call-to-power-2/ctp2-creation/9437883-making-cradle-3-fully-compatible-with-the-apolyton-edition
Just give a ship all the Worker flags. I've read that someone has tried it, and it seems to work. The only thing is though, that if the AI builds them, you'll eventually end up with railroads on your water squares.
If you make a new air unit, but you don't activate the "inmobile" property it will be able to move over land & sea, and to attack units of both types. The only drawback to this is that there is no corresponding AI strategy, so the computer player won't be able to use this unit well (haven't actually tested this last part, but it's a logical assumption).
You're right in saying that Firaxis should give us the ability to choose on which terrain each each unit can move.
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