I played XD:Gale of Darkness and its predecessor whose name I can say but not spell(lol). I would like to see a similar system concerning Shadow Pokemobs in this mod if possible, but I have no clue if it's actually feasible with your current Trainer NPC code. The system I envision would work something along the lines of this:

When certain conditions are met(conditions I was thinking of explained further down), a trainer NPC may add a Shadow Pokemob to their roster. This Pokemob would be somewhat stronger than the rest of the trainer's Pokemobs, but nothing too ridiculous, and would know nothing but Shadow moves. Its species would be determined by the biome, anything that can spawn in the vicinity of where the trainer was when they added it has a chance of being selected, perhaps barring advanced legendaries. It would also give off a purple particle effect, and the shiny chance for said Pokemob would apply at the instant it is added to the trainer's roster, there would be no change in shininess in between battles with said NPC. Now, in order to obtain this Pokemob, one would need to use snagcubes, which would disable the "no thieving from trainers" system, but only when used on a shadow Pokemob.(Note: a shadow Pokemob owned by a player would not be snaggable, only ones owned by NPCs.) After a Pokemob has been snagged from an NPC trainer, it will be removed from their roster, however if one fails to catch the Pokemob it will still be there next time the Trainer is rematched. A trainer may take on more than one Shadow Pokemob, but the chances are greatly diminished with each one added so as to stop trainers having 20 Shadow Pokemobs or crazy stuff like that.

Once snagged by a player, a Shadow Pokemob will be unable to gain levels until being Purified, which is done by fighting battles with said Pokemob until a bar under its health reaches zero, then shift right clicking a Celebi altar with an empty hand while said Pokemob is standing nearby. While a Shadow Pokemob, it will be permanently set to Guard Mode, and cannot be told not to attack, however it will not target its owner on purpose. Once Purified, it will forget all Shadow moves and learn a random set of moves: three that that Pokemob can learn normally or through TMs, and one that is randomly selected from a separate list of moves common to all Purified Pokemobs, and applied to that Pokemob regardless of whether it can learn that move or not. It will then be able to be taken off of Guard mode and told not to attack in the same fashion as other Pokemobs.

Now, back to how NPC trainers actually wind up with Shadow Pokemobs in the first place. Different classes of trainer have different levels of "shadiness" for example a Burglar would have more than a Lass. If a trainer is positioned near to a specific NPC(rarely spawned in all biomes, will run from players, and will not talk to a player even if they catch up.), and has been defeated by a player recently(sparking anger and desperation to win next time), they may interact with this NPC. The chance they will approach this character is determined by their "Shadiness" level, and the chance this character will answer them is determined by how many Shadow Pokemobs they have(More mobs=less chance). If the transaction goes through successfully, the trainer will have a Shadow Pokemob randomly selected from wild species of the surrounding area in their roster next time they are battleable.

Now, under certain circumstances a Shadow Pokemob could spawn wild, an example being XD001(Shadow Lugia) spawning from a wither build on a No-MC-Mobs world. In this case, the mob would still only be catchable with Snagcubes, the only difference being that if it is defeated, it must be spawned again in order to be rebattled.

This is the best idea I could think of for Shadow Pokemobs, but if it's not feasible, I'll do my best to think up something else for you.