I subscribe to the new Feng Shui adventures, and they seem to all be about the cyber-apes.
I don't use the cyber-apes in my game, but I use all the other factions. In my world, the future juncture is more Mad Max-meets-Alita Battle Angel. It's a post-apocalyptic world ruled by cyborgs and wasteland warriors. I just find the punny cyber-apes don't appeal to me, so I've excluded them.
Will there be adventures that don't involve cyber apes?
I am not an Atlas games publisher but I will throw in my 2 bits opinion
Technically the first adventure doesn’t have the New Simian Army as the key antagonists - it is Eaters of the Lotus.
I haven’t read the third adventure (though the title does mention Ape, Arts and Arson)
The key thing is that the published adventures take from the factions in the Feng Shui world
The New Simian Army and the Eaters of the Lotus are your obvious baddies to smack down. With the New Simian Army being the replacement to the Architects (who I never really used in my feng Shui 1 games)
There are opportunities for The Ascended and the Guiding Hand to make an appearance in future published though both would be challenging as they operate in clandestine ways putting the secret in SECRET WAR.
Of course, there is nothing stopping you creating and swapping out the New Simian Army for a different group of antagonists but what is their key goal in the Feng Shui 2 world (destroy everything, end the world, etc)
The original fun with Cyber-Simians is their wacky codenames:
Battlechimp Potemkin
Furious George and the Flying Monkeys (featuring Apeshot, Marmojet, etc.)
Orangutank and the Chim-panzers
Koko Chanel (High explosives go with everything; "Does this rocket-launcher make me look fat?")
Clockwork Orangutan (a malenky bit of the old monkey-violence) [1850s Juncture]
Funky Monkey [1970s popup juncture]
Pontius Primate
...sure, the names are cute. I'm just not into it, myself. I love all the other factions, I just don't use the apes.
I've always found the future juncture to be the weakest and I think it's because it doesn't seem to have much depth of Hong-Kong cinema behind it. Unless there's a whole stack of future dystopia films I'm not aware of. (This is quite possible, my knowledge of Hong-Kong cinema is not that strong) The only film I can think of which has any sort of sci-fi element is "Heroic Trio" and its sequel.
Maybe a filmography would help. Of course now that it's largely post-apocalyptic that opens up your potential source material.
I personally have fleshed out my future juncture quite a bit, based on a combination of Mad Max's word and other stories like Battle Angel Alita and Mortal Engines. I've got multiple factions of wasteland warriors and drivers as well as a faction of free cyborgs and a warlord with a huge walking city who roams the wasteland with his own cyborg warriors.
If you don't like the monkeys, then I recommend swapping them out for gangs of cyber-junkies and body-modification freaks.
There's a lot of dystopic films, the future part less so. Science-fiction was not an especially popular genre in HK media historically. Generally speaking, though, you can map any contemporary era cops-and-triads movie into the Architects/2056 setting pretty easily. These days you can just use the local news; fiction is no longer necessary for dystopia.
Here's a few suggestions, some of which are more relevant for urban cyberpunk scenarios and some for after-the-chi-bomb post-apocalyptica. As is common for Hong Kong movies, the tone ranges from absurd and comedic to very serious. The Wikipedia summaries, sadly, are often very brief, but you can find more detailed descriptions at sites like Love HK Film.
Yeah! They are really funny! 
I've always been fond of Kurt Wimmer's Equilibrium as a good aesthetic for the 2056 dystopia. And I was always rather curious as to why the Killer was not an available archetype for 2056 in the first edition -- the Buro strikes me as making plenty of use of assassins themselves, and they serve as quite the formidable agents for when Public Order would be too loud and obnoxious for the job, much like the Grammaton Clerics from that movie. Bring on the gunkata, I say!