See that was my idea exactly I mean for the most part by late game you wont really have any ships anywhere NEAR your core systems unless you are building them!!! or unless your empire is losing the war (which of course happens once and a while).
I mean for example in the unmodded game I'm playing right now I have zero (0) ships defending my most heavily populated worlds but I have over 600 ships out there pillaging and rampaging across the 400+ worlds of the Earth alliance!
I would love to have to worry about pirates and marauders and smugglers as that would add some spice to my game as right now it's just a matter of my invincible fleets conquering across the galaxy one system at a time (or nova bombing a system that is too heavily fortified hehe) until eventually I reach the end of the game, as it is the EA is no real threat to me anymore and I miss the days of the early part of the game where my empire was beseiged on all sides and from one turn to the next I didn't know if my blockades would hold or if the enemy would manage to slip into my space and depopulate one of my precious few worlds, now I have 18 Sphere worlds, 400+ planets a population of 1.8 trillion a fleet of over 600 ships and have only conquered have the galaxy as the EA has the other half.
Pirates would add flare to the game yes but more then that i think they would also prevent the true feeling of an uber empire because you would always have that "what if this turn a pirate attacks and one of my core worlds is enslaved?" or "What if this fringe world turns into marauders and tries to conquer their system?" you would always have something to keep you on your toes.
Now although I beleive pirates should be a rather common thing I think things on the scale of worlds rebelling and Marauders coming in should be a limited thing this way you don't have SOOOO many raids on your space that it ruins the game between you and other players or the computer races. But in vanilla a world would never rebel without years of riots and even then it was iffy I think fullout rebellions on rioting worlds SHOULD take place and maybe they could bring a few of your warships over to their point of view and try and carve out their own little empire.....as it is any rebel worlds I've ever seen surrender in 1 turn and never build any form of military or defenses of their own.
But if you think about it Marauders and pirates could ALSO act as a new sort of diplomatic thing say if you see pirate ships you can hail their captains and ask them to support you against another player or something and see if you can bribe em

. But more then that say if Player (A) and player (B) are allies and player A is plagued by pirates (A) can ask (B) for aid agaisnt them and say give a "gift" in the form of resources to encourage such an action.
AND THAT'S Another thing I'd like to see Cold hard bribes! Like in Civ where you can demand X ammount of money from them to do as they ask or they can demand X ammoun of you to do as you ask this would much improve the game instead of just those stupid "Aid us against empire blah blah" which the AI NEVER DOES because it has NOTHING TO GAIN......but anyway that's another story hehe.