IMO, the major difficulty in (re-)balancing everything is making all options viable without making them identical (i.e., all damage/tonnage/reload formulae exactly the same, etc.). If you can pull it off, I for one will tip my hat to you.
I like the destroyer carrier idea. It has good elements of surprise, at least the first couple of times it's tried. Never building more than two or three of the same ship name (i.e., rename designs every turn) also helps with that. And ISTR reading the "use light carriers as early game heavy-weapons bases" idea before, but that doesn't make it any less effective. Anything to throw the opponent off-balance, even if it is tactically implausible in the long term, is a good idea IMO. At least against humans--the AI doesn't know the difference.

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The Unpronounceable Krsqk
"Well, sir, at the moment my left processor doesn't know what my right is doing." -
Freefall