I wish there was more of them and they were even worse. I don't care for the Dark Souls style, IWTBTG level of difficulty in a whole game, but I don't mind there being a super secret optional challenge, I love that kind of thing. I wish that activating the Hypershunt opened up a portal in the system you use it in and Ultra-Redactoids would randomly pour through leading fleets of Remnants so I could have a semi-regular source of superweapons and overpowered unfair boss fights.
In StarSector, once you're in the endgame, you choose your own difficulty level. I never considered the eldritch horrors of hyperspace to be all that difficult, since by the time I needed the hypershunt or could remotely afford to repair it, I've always had multiple size six colonies. Oh big deal, this fight's too hard, I might have to throw half my industrial production for a few months at it. O woe is me, since I can only build one and a half paragons a month it will take three months to replace the gratuitous losses from that fight. I feel a little bad about the thousand or so imaginary crewmen that died as I casually threw reinforcements at a fight like a WWI general, less bad about the imaginary shareholders that will get slightly smaller dividends this cycle. My point is, by endgame, casualties from any fight are just a rounding error in my profits for the month since I can crank out battleships.
If this battle is too difficult, cheat. Crank up the battle size to whatever your rig can handle. I usually have my battles on 500 to look properly cinematic like the background of a Star Wars action sequence or whatnot.
I use the Ziggurat as a novelty, not as a main part of my fleet. I bring it out to take on truly overpowered boss fights from mods, but my standard Tesseract fighting fleet is a Tach Lance Paragon, a beam Aurora, and (piloted by your humble narrator) a Safety Overrides Triple Heavy Blaster Aurora. I've also pulled off the battle with only cruisers as part of a challenge run, I think it was two Dominators, two Champions, and as many Auroras as would fit in the battle. Admittedly on the cruiser run I used a ton of S-Mods and had some really good luck with the hidden weapon cache. I think I had two of the lightning PDs and one each of the small and medium antimatter missiles.
Man you want an overpowered unfair boss fight go play the Xhan mod and fight Thousand Eyes. I wish Thousand Eyes was part of vanilla, or at least vanilla had something that rule-bending and unfair. I wish vanilla had some Evil Otto kill-you-in-real-life Absolute Virtue Pandemonium Warden type dude to fight. Something's gotta be making those slipstreams in hyperspace after all.