April 1st is just a coincidence.
I mean, your OP:
For example: hundreds of clearings of cultist lairs, skyscrapers filled with enemies, vast caves with complex labyrinths, and so on and so forth.
You're doing something totally wrong if there are "hundreds" of clearings of cultist lairs. I guess usually you have a dozen or at most two dozen missions per initial cult (most of them the initial apprehension and safe house missions). These are not really all that repetitive, because you will have killed off the cults by the end of the first year or so. If they keep popping up for years, you're completely mismanaging the game and deserve to be punished. For advanced cults, there are much fewer missions.
I actually think the first year of dealing with scarce resources and taking down initial cults with agents in training and poor-ish equipment, when agent or squad wipe is always lurking around the corner (SH/IM), is one of the most interesting parts of the game. You lose much of the excitement once you get into the midgame and you get almost invincible if you know what you're doing.
I think there are exactly two skyscaper missions. Syndicate Data Seizure (where you don't necessarily even need to enter the building, I usually don't) and Syndicate Regional HQ. Both need to completed only one time. In the latter you don't need to enter the scryscraper either, if you blast enough holes on the walls so that the walkers and other enemies jump down. Hardly a nuisance. These missions are actually on the more interesting side.
Vast caves with complex labyrinths is also not that big a thing IMO. Zombie Hives are the only ones I very regularly just skip (very small penalty), because the maze is just rather boring and it can be quite dangerous. On the other hand, Zombie Labyrinth is a very open and easy mission. Also for example Syndicate Monster Lab mission has some catacomb parts but those are usually rather straightforward and you will just need to deal with a couple of stragglers in the labyrinth part.
So while there certainly is some repetition, this is IMHO much better than, for example, repeat missions of various UFOs in the vanilla.
