At the moment pirates are nothing more than an annoyance for the first fifty turns or so when you have the bad luck to encounter them that early:
- Their ships never move more than 2 tiles per round (as far as I remember my games, although I have to say I didn't play a lot of them yet because my games normally last many, many hours each).
- They never have a lot of ships.
- Their ships are always weak (them seem to get a little better when time passes, but not much).
- They never do much besides attacking ships of fleets that happen to literally stumble over them.
It shouldn't be too difficult to tweak them a bit so they actually pose a threat, e. g.:
- Give them faster ships from the beginning, with greater sensor range.
- Give them more and better ships (increase production capacity of their shipyard, give them more than one shipyard), let them inprove their ships at a faster rate.
- Let them not only attack nearby ships, but let them raid planets (attack a planet, if defence is defeated, take some credits from the treasury and go back to their base; use the money to build even more ships).
- Let them hide their bases in nebulae and give them the ability to be immune against nebulae effects.
- If the new Scavenge ability in the game, that's an ideal ability for the pirates to snatch ships for themselves when attacking ships and fleets.
- Even give them the chance to get a tech if they scavenge a ships with techs they don't own yet.
- Give them variety, that is there is a certain chance for all of the above abilities and possibilities to which degree an individual pirate group has those.
- Give them personality by giving their leaders a face (that is, portrait) and showing messages, possibly with choices ("We have wiped away your puny defence fleet at Larion III and enjoyed our stay there so much that we will surely return soon, har har!" or "We are showing your precious governor of Keri our hospitality at the moment, but for unknown reasons he prefers to return to his world soon. To account for our expenses to deliver him there please be so kind to send us the moderate sum of 2000 credits." -> if you don't pay, the governor is killed and with him all bonuses he gave to his world).
And if you think about it there are surely more possibilities here of which I didn't think yet 
