Hello!
I remember the Homeworld games (I can't remember if it was the first or second game) had some very unfair difficulty scaling which was based on the amount of resources you collected and your fleet size.
This means that if you played the game as a proper RTS, where you wanted to collect as many resources as possible and invest those into building a good balanced fleet to tackle space combat, you were facing more & more difficult enemy fleets. It would also lead to unintuitive strategies, where you wanted to keep your fleet as minimal as possible in order to not face unfair challenges, since the later missions could get close to unfinishable by playing normally.
While I understand the concept - making the player focus more on proper play during tactical combat engagements - it invalidated for me one important layer of RTS games, which is resource management & base/fleet building.
It's also very funny, since it made actual speedruns much easier than playing the game normally/strategically.
Other than Homeworld, the genres where unfair AI was most present were roguelikes/procedurally generated games or RPG games with difficulty scaling based on character level/power (which by the way I find to be terrible game design, since it completely destroys both immersion and RPG character progression).
Nice topic!