[Nitram Draw]

I don't think it will ever be possible to get the AI to use all the available tech/weapon combos effectively. As you point out they are only as good as their creator made them. The AI, in its current state, can never learn. This is really what must be changed to make the AI much better. The game is so complex and there are so many variables that it is impossible to program the AI to take advantage of them all.
So far most of the good modded AI's have made compromises and are worthy opponents in the short term. The longer the game goes the easier they get to beat.
Some of the mods have added the minesweeper ability to an item that also has other uses, Dev mod gives this ability to PD cannons. This is a good compromise I think. While a human will always build dedicated minesweepers and include them in the fleet the AI just won't.
Plagues are another area the AI is weak in, if it's not in the program they will just die. The medical ability could be given to something the AI will definately produce.
The only problem with the compromise approach is it dilutes the thing that makes this game great, the variety. Maybe MM will take everything learned/suggested in this forum and use it in SE5 to make the game that this one could be. Don't get me wrong, I LOVE this game. I just hope the next Version has a big improvement in the AI.