The details on what I attempted in the mod-
-I slowed the trade and refinery ships from 300 to 150 to give the pirates more chance to destroy them, though I still consider that they might have too much health. I also increased the rebuild time from 12s to 300s so that the destruction of a trade ship had some sort of financial impact.
The pirates can then be directed in small groups to attack remote trade planets rather than the front line, the outstanding problem being when they have to pass starbases. I would have made them immune to damage from jumping out of starbased wells, if I could.
-I couldn't place the pirate base in a plasma storm as I wanted, but as I considered allowing the pirate turrets to have flak burst to be too strong (and there should be a graphic upgrade) I went for jam weapons instead. If only they could have a phase jump inhibitor!
-The pirate armour modifiers were silly, with pirates only vulnerable to heavies, I made them more reasonable, typically 0.5 rather than 0.3. I also limited them to 8 upgrades at 0.05, rather than 10 at 0.1, which prevents the ridiculous armour figures and makes the turrets destroyable in a reasonable amount of time, even late in the game.
-The ability research doesn't seem to work, so I couldn't copy it. I added abilities as follows: all pirate ships gained unstoppable phase jumps, all but the cruisers became able to cloak. Scouts got Detect Mines, Timed Charges and Sacrifice- though I couldn't add a comment like 'Made it Ma, top of the world!'. Mediums I added an antimatter cripple, Siege Subversion and Flak Flakburst, though this is very heavy on anti so they get only one shot. Cruisers had to have Domination for the pirate captures! This can be very tricky because of the potential for Rapture abuse, but I made it so heavy on antimatter that it couldn't be used after a single jump, so that the cruisers can only block gravwells.
-I reduced the pirate raid sensitivity to planets and upped sensitivity to trade and bounty, so they they appear in greater numbers only when it is warranted. I also cut the heavier cruisers and siege out of the smaller raids entirely. However the pirate missions can still be very effective if targetted properly, and not used as a temporary second main battle fleet.