I normally avoid the Evil Team trope – while events caused by the canon Teams may be brought up as incidents that occurred at some point (and even then there tend to be conflicting accounts about the specifics), the world of organized crime in the Pokémon world does not really appeal to me as a story vector. Indeed, my two active fan-regions do not have their own evil teams – Miato's major adventure element revolves around the mysteries left behind by the ancient advanced civilisation that once lived there and their symbiotic quasi-living technology, whereas Norrvalo is a small island with a relatively small population and very few problems. That is not to say I've not frellled around with the likes before, though...
At the End of the Wilderness, My aborted Orre fic, had an offshoot of Cipher that claimed the name after the dissolution of the former. Much like the original Cipher, they were all about the Shadow Pokémon research and had legitimate front and members at high places. Where they differed however was their motive – Wilderness!Cipher had an almost cult-like devotion to the idea of transcending feeling, emotion, bonds, pain – all of which they viewed as limiters keeping Pokémon and People from attaining their true potential – an ideal that Shadow Pokémon embody. Building on the Shadow Pokémon technology developed by their predecessors and seeking to compensate for its flaws, they turned to nanotechnology, essentially creating a self-replicating, infectious vector that was not only transferrable between specimens but also remained in the system even after standard 'purification', restarting the process that turns a Pokémon into a shadow Pokémon even after it was purified – and ultimately sought to develop a human analogue of the same contagion. One of the key individuals behind this incarnation of Cipher was also the founder and owner of a company ostensibly conducting archaeological research but actually deeply connected with whatever passes for government in Orre (a tenuous concept as is) and contracted by the same to figure out some kind of a massive ancient device discovered in the deep desert which may or may not be a supercomputer, a terraforming device, a superweapon or all of these things at the same time, left behind by a native civilization that essentially created the Regis. (Hey, it was still gen 3 when I started that fic, gen 4 was actively JUST starting to show up and the giant marshmallow that is Regigigas was not fleshed out yet!). Said Antagonist was actually playing all sides against the middle. The Government shenanigans granted him access to a device he very much wished to manipulate for his own private ends. The corporate front was used for legitimate engagements, whereas Cipher (whom were operating under the assumption that the Great Machine could be used to release their shadow-nanoparticles en-masse throughout Orre and then the world and maybe even perform the calculations required to make this nonsense work on humans) were used to perform some of the truly dark shit that the big antagonist needed to pull off (which involved a fair bit of kidnapping of children with a particular technopathic psychic potential identified through government records at a very young age and giving them the right sort of interface implants so they could 'tune' the Great Machine, quite against said machine's will). Ultimately though I'm pretty sure that his ultimate goal was to release a wholly different type of nanomachine cloud, one that would subject the entire region to his will rather than "free them from emotion" as Cipher thought or hand a means to control it over to government backers. Of course, he thought he had failsafes for his failsafes, but somehow it all kind of fell apart due to a convergence of characters, each of whom had encountered a different front for his ambitions, and all of whom ended up crucial for unraveling it...
... And of course, he had a Pokémon team based on the seven deadly sins, with Snorlax pulling double duty as Sloth and Gluttony to make six.
I dunno. It all sounds like a huge mess, because it was. A big damned JRPG-powered mess. I realize it's not exactly a "new" evil team, but that's probably the closest I got to in the realm of fic.
I guess that if i'm throwing RP into the mix though there would also be Project Rising Helix, an even older and dumber concept of what started out as an innocuous research group studying Pokémon genetics, sequencing Pokémon genomes, that sort of thing, ran into financial trouble, then got a new shady backer who brought in some rather unscrupulous specialists for "procurement" of samples (from strong or Pokémon of particular potential – regardless of whether it's wild or owned, and if anyone has to get badly hurt for them to acquire a sample) and was essentially trying to put together augmented Pokémon as bio-weapon and the means to control them. Their flagship project was some kind of a black-scaled Salamence... thing that ran absolutely rampant when its 'pilot' lost control due to neural feedback from the forced artificial synchronization she used to control it. Even more disturbing was probably the chimeric mess of three dittos that they forced to fuse into a singular entity that is one mind in three bodies and can control up to three separate morphs at once, sort of designed as a big damned boss for an encounter that was meant to involve all three of the main playable characters and their starters and mark the point where said starters evolved from their mid form to their final form. Mutant dark counterparts and all that. Edge and Cringe? Surely. But it was 2003 and I was younger and much dafter. And to be absolutely fair for me, Rising Helix's Modified Getaway Alakazams were cool looking as frick.
....
Either way yeah. That's all the Evil Teams i've done and probably all the evil teams I'll ever do. <<