Right now, Thargoids are the only thing that has any kind of challenge but I can't use my engineered weapons and I have to find for mats for premium synth to do it, which is extremely lame.
Not to mention that "big tough bossfight" is way less interesting to me than "absolutely gigantic furball".
I loved the original wing assassinations for having a moderately-tough big-three mission target and an absolute
pile of unengineered escorts. Sure, the escorts popped easily, but there were enough of them to pose a serious threat just from the sheer number of shots they could pump out. There was variety in their wings. You had no idea what the target would be or what engineering it would have, you had no idea what the escorts would be.
Now? It's a FDL and some vultures. Every time. Every single time. Even spec ops have more variety. The escorts are as annoying and tanky as the lead ship, and often they're pushing out
less damage when they focus you than the original missions were - sure, the vultures are engineered, but at the end of the day it's just 1-3 small ships firing at you. Before, it was like half a dozen escorts, at least one of which is FDL-sized. They
hurt if you let them focus you.