First off, I apologize in advance for laying down mighty Wall-O-Text.  Likewise for getting up on a soapbox and preaching proposed changes be made to the game.  But I only do so in the hope of making an awesome game even better.  I do hope you'll forgive my hubris and give the issue some thought.  So without further ado:

It just doesn't seem right that pirates can bust up a fully fortified planet and its complete fleet(plus mines) due to a never-ending increase in stat scaling.  Some of the ships are just silly too, like Pillagers having 12,000 range or whatever, and getting what I can only guess is an anti-structure attack modifier against buildings.  A fully upgraded Advent starbase with all offensive, defensive, and meteor control upgrades along with 45 tactical structure slots shouldn't lose to a basic raid.  That says nothing of the stupidly massive 100+ ship raids you can send out through pirate missions(which is happily fueled by the TEC's Worthy Cause credit boom tech) every 5 minutes at any target of your choice.  In many ways, it isn't even worth building your own fleet to take on enemy fortifications, the pirates have better ships than you could ever get.

The only good side is taking a 2,500 supply fleet to the pirate base, usually populated with 500+ ships at that point, to duke it out for 15 minutes straight(or more).  I lost 100 ships last time doing that, about 600 supply.  But, that was using an end game Advent fleet carefully managed throughout the fight.  I'm sure others would have suffered greater losses.

As it stands now, the Vasari don't need to fear the unknown force pursuing them for thousands of years.  Instead they need to convince the TEC to throw 1,000,000 credits at the pirates to assemble an armageddon force capable of taking over the whole damn galaxy.

I like having more pirates, and I like them being stronger.  Pirate armadas are fine by me.  What I don't like though, is for them to become stronger than any military force in the game.  Pirates need to diversify into economy destabilization.  Make them have a maximum ceiling for strength.  Instead they should get a bunch of new techs to slow the economy of their target.  One example might include new 'raiding party' ships.  These ships would attempt something similar to the Subversion of the Vasari's Maurader.  Essentially, it would have the ability to 'colonize' and 'capture any extracter'.  If a planet is colonized, half of its income is stolen and build rates are reduced by 50% for 10 minutes.  If an extractor is captured, all of its income is stolen.  Furthermore, it has to be destroyed and rebuilt.  Pirates should have other abilities to capture trade ports and refineries; similar to the planetary subversion.  Feel free to call these new ships Buccaneers, Hijackers, or Ravagers.

Actually, A full revamp of pirates might be in order.  To reiterate, pirates should be about disrupting an economy, not overthrowing an empire through military force.  To that end, each pirate ship should be able to specialize in some way toward that end.

*Corsairs are the traditional anti-structure ship, and that is supported in part due to their new Gauss Rail Guns.  A group of these should be able to chain their ability to whittle down a starbase over time.  Likewise, they should go after soft targets like repair structures and hangars.

*So Pillagers don't need to function like Ogrov Torpedo Cruisers anymore.  Instead, Pillagers should have Nuclear Fallout when sieging a planet.  Maybe they reduce population growth by 80% for 10 minutes.  Combined with the high 'population kill rate' for siege frigates, this would put quite a damper on your economy and make them high priority targets.

*Cutthroats already have Plunder.  This makes sense, since they're giant trade ships.  In addition they should get Bribery, which would be the skill to capture part of the income from tradeport and refinery structures.  It would last for 10 minutes.

*The proposed new ship I suggested could use a modified colony frigate skin.  It would have Subversion and Capture Extractor as abilities, as already mentioned.  So even if you chase off the Pillagers, your economy is still being tanked for a period.

*The Rogue needs a new ability as well.  I suggest Sabotage Structure.  This tech would 'silently', at least if you weren'twatching the ship when it triggered the ability, plant explosives in one of your orbital structures.  After 10 minutes, the bombs would go off, destroying the structure.  To make it fair, the tech would be a 'channeling' ability active for 60 seconds while the strike team attempts to plant their explosives.  If the ship is destroyed during that time, the bomb threat is averted.  This is great because Rogues are small, fast ships that might otherwise go unnoticed by the enemy during large assaults.

*Why leave the Reaper out of the love?  Well, most of the disruption is already covered.  But Reapers need a nice niche too.  I suggest something a bit more basic for them.  Microwave Burst.  This ability would have a high cooldown, maybe five minutes, but would reveal 2-4 mines within a range of 5000 when triggered.  This mines revealed in this way would be random, limiting the effectiveness of the skill somewhat.  But if you have 10 Reapers, they could potentially reveal 20-40 mines.  This also fixes the current bug in the AI where pirates sit idly in gravity wells with cloaked mines FOREVER.  On the flipside, until all the mines are revealed and destroyed, the pirates will continue to camp in that gravity well: essentially daring anyone to take them on in combat.

So imagine the scenario:  A pirate fleet jumps into a defended system.  The Reapers expose 20-40 mines and destroy them before moving on to strikecraft defense(and anti-LRM duty).   Corsairs sail into the gravity well, busting up a repair structure on the way to your starbase, where they take turns crippling its passive regeneration.  Meanwhile the Ravager(proposed new ship) has captured half your taxes and has taken over  your resource extractors, in addition to slowing the build rate for your immediate response.  Cutthroats have stolen your income fromh tradeports and refineries, and are busily Plundering and destroying econ frigates.  The Pillagers have also begun bombing your planet and killing your populace en masse.  Your defenses beat them off, but perhaps while fending off the Pillagers you forgot about the Rogues.  10 minutes later a military lab and frigate factory suddenly explode.

In such a system it pays to consider fortifications on pirate-bordered worlds.  But that doesn't mean a crafy player might not send the pirates on a mission with a massive armada to smash through to your home world.  At the same time though, you could set up a network of Phase Jump Inhibitors to slow down the pirate assault and respond to it in a timely manner.  Pirates are a constant concern, but they aren't going to single-handedly overthrow your entire empire by having 5,000 hull points, 50 armor, and 100 attack power per ship(now with their new super-secret "pirate armor" that resists traditional damage).

On a side note, pirate base defenses are fine, with the turrets covering the whole visible gravity well and having a super Flak Burst function to take out strikecraft.  I'd even go for them having the TEC's Planetary Shield structure unlocked and in use.  That stops you from using the Novalith to easily take them out.  In exchange, their Plundered Booty bonus should be increased to 10.0 credits/second, to pay for the massive assault needed to take over and colonize a pirate base.