Finding too much fault with Sins of the Solar Empire is rather difficult, but one consistant complaint that I could come up with is the Pirates.  The concept is nice but, to me, not well implemented.
Early game pirates.  Start with a few dozen frigates that have the ability to "tackle" player/AI ships.  Tackle, meaning, cripple the ship, board it, take it over, and finally, tow it back to it's base.  This should be done rather infrequently.  Once back at the base, the "tackled" ship can be used to create credits for the pirate base, or credits used to repair/refit the ship.
Another early game ability should be scout/trade-ship raids. These raids should consist of the Pirates destroying scout ships and trade ships of the player/AI.  Each ship/trade-ship destroyed would net the pirates credits as well so that they can keep up their economy.
And finally, a last early game goal would be mining raids.  Capture mining facilities of player/AI.
Late game pirates, should concentrate on structure runs.  Destroying, infrequently, some offensive/defensive/economic structure(s) that the player/AI has.
Pirates should never go for planet destruction, for that would be detrimental to their livelyhood.  Pirates are in it for the money, not the glory of conquering.

These are just my thoughts.  What say ya'll?