There is nothing in here that makes me care about the characters. In the first sample, they both wander into HQ, but they don't come across as upset, interested, surprised, confused... anything. There's no emotion there at all. Just he said/she said dialogue.
I can see you're aware of that being a problem and have tried to work on it. You've managed to avoid them being literal talking heads - there's a fair amount of movement in both stories. But none of that is translating into emotion. Take a look at these examples:
“What? Normally, humans just catch us in a Pokéball.” Shadow glared at Canopus. “If you try, I will make you stop.”
Canopus picked Shadow up, causing him to struggle.
“Put me down!”
“Fine.” Canopus placed him on the floor.
Why did Canopus pick Shadow up? Because he was annoying? Because she wanted to show her strength? Because she found it funny? Absolutely no idea. And why did she put him down? Again, there's no emotion there - it feels like "Verbal input 'put me down' received; executing command."
“... Shadow, the food’s worse than what I had in Tokyo and that’s saying something.” Canopus slapped the hand away. “Trust me on that one.”
Shadow frowned before focusing. A pile of toxic waste appeared in front of the door.
“Are you trying to dissuade me with that?” Canopus raised an eyebrow. “Some demons are worse than that.”
“Like what?” asked Shadow. Canopus pulled out her phone.
“Well, there’s Foul Slime, for one. Look.” She showed Shadow the picture.
“Okay. that could be worse. Anyway…” Shadow blinked and both the door and the console disappeared. “I’m not letting you go.”
This one goes even more into the no emotion. Shadow has no reason for creating the pile (I assume that was an attack? Or just an illusion?). Canopus doesn't find it amusing, or mildly disgusting, or contemptuous. Shadow has no reaction to being flatly rebuffed, nor does he find the picture she shows him disgusting, informative, horrifying... anything. "Visual input received; executing next dialogue."
Then there's the dialogue itself. It looks like you're suffering from what I usually call Cowrite Disease, where both characters try and cram as much information as possible into their dialogue, and reply to everything. Only... people don't work like that. If I walked up to you and said "Hi, my name's Huinesoron, how are you doing? Also would you like a cookie? And by the way, I've got this new story you might like to check out, what's your email address?", you'd a) think I was crazy, and b) say something like "Uh, I'd love a cookie, thanks... what's this about a story?"
What you wouldn't say is: "Hi, I'm CodeCom, I'm doing fine. A cookie sounds nice! Anyway, wow, I'd really like to read it, here's my email address. By the way, what's your favourite colour? And have you ever played any Pokemon games?"
Now look at this:
“What?!” the grey demon spun on its four legs. “I’m a Pokémon, not a demon. Whatever that is.”
“Trying to lie, huh? I’m pretty sure you’re a demon, though I’ve never seen one like you.” Canopus pulled out her smartphone and flicked to the Demon Summoning App. “What happened to all my demons?! What the hell?!”
“I’m not a demon! I’m a Zorua!” the demon took a few steps back. “And there’s no need to threaten me. Everyone knows what a Pokemon is, at least.”
“Well, I don’t. And it doesn't matter what your species is, that still makes you a demon.” Canopus glared down at her smartphone. “Great, I’m also stuck with all the weak skills. Why am I telling you this anyway?”
It's not quite so blatant as my examples, but you've definitely got multi-threaded conversation there. It's a very easy trap to fall into, because that is how people talk online. A lot of my early missions do the same thing (and co-writes are particularly prone to it). But it also feels nothing like actual conversation.
Okay, so at this point I think it's clear I'm going to say Permission denied, but don't let that dissuade you! You're doing an awful lot of things right. Your spelling etc is good; you've avoided Talking Heads Disorder (well done!); you clearly know a bit about PPC HQ; you've managed to keep your characters consistent across two stories. A bit of work on getting them to talk like people and react like non-robots and you'll be set. (For the former, try reading the dialogue out, and work out what you'd say in response; if you'd like, I'll scribble down some 'faux-Shadow replies' to Canopus' dialogue in the first story, to show you what I mean.)
Moving on to some other points I noticed:
-It's standard in online writing to leave an empty line between paragraphs. If you don't want to do that (for some reason?), at least indent the first line; it makes reading much easier.
-When you fixed that line Bramandin pointed out, you left it as 'I only work with people only for a mission.' That's two 'only's in a row, which sounds super weird (read it out!); I think you were originally aiming for 'I only work with people on a mission'.
-'Shadow stalked over and punched Shadow in the face.' Shadow, I know you can make illusory copies of yourself, but don't get carried away. ;)
-Looking now at your bios (I tend to avoid them until I need to read them; I prefer to get character information from the stories):
--Both your characters are presented as being interesting primarily for their emotions, and the interplay between them - reserved Canopus (who has a hidden fun side) and playful Shadow (who can be irritating when he doesn't shut up). But... well, see previous comments about emotions in your writing. The only reason I know from your stories that Canopus is reserved is that she flat-out says it. Ditto for Shadow being a prankster. It's a really interesting dynamic you have planned, but right now it isn't coming across in your writing.
--I have no problems with the powers and backgrounds; two things, though:
a) Canopus is a trained, jaded, scarred and emotionally-battered professional at 17? Is that... common in her 'verse?
b) Do Zorua normally have names? Most Pokemon don't unless they're captured. I remember having this same conversation about Skarm's agent Falchion.
--Be aware that we have another (mute) Zorua in HQ.
--RC numbers are normally... well... numbers. Check the list. '4SMT4A' strays quite a bit further from that than normal.
-I have no issues with the badfic you've chosen.
If anyone can offer better advice than me on the emotional issue, I'd appreciate it; I'm aware that I haven't been very clear.
hS