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If you've got energy constraints it may be a better idea to scrap the science ships when they're done researching, after all they take something like 2000 energy.
Mark IIs, because they have cloaking, are also good to peek into AI-controlled ARS systems to see what you can get from a Ship Design Hack. Mark Is are prone to die when you try that.
Could have swore they were once able to be placed in a transport. Maybe my memory has failed me.