My P&N suggstion: (Wot I 'ave suggested elsewhere before)
Give crew quarters boarding party abilities. That way you can take over enemy ships from the very beginning of the game, and you have a reason to design ships with a little CQ redundancy. Of course CQ boarding defence would be considerably higher than CQ boarding attack.
The only downside is that your specialised boarding ships will lose their crews when they board. Unless... You make a second CQ component available when boarding parties come into the game - one which has no boarding attack value. Then you could design specialised boarding craft with good old fashioned non-destroying crew quarters. If you made these available from the begininning though you might as well make boarding parties available...
Another suggestion (specially useful given your new approach to resupply) is to add a few more tech levels to the solar harvesting tech tree: After solar panels and solar sails, add solar sail-panels, which generate movement AND supplies. I think you'll definitely need some new supply generation options.
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L GdY $ Fr- C- Sd T!+ Sf-- Tcp-- A% M>M+ MpD! RV Pw Fq+ Nd- Rp+ G-
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