Moképon/WMG
There's a connection between the disappearance/deaths of Ash Ketchum and Gary Oak
Think about it. Assume that the comic takes place in 2009. Kahn mentions that Gary disappeared ten years prior. The date on Ash's statue? 1981 - 1999. 1999 being 10 years before the comic, the same year of the other's disappearance. The two incidents are probably related.
Masked Dude IS Gary Motherfing Oak
Not sure of his motivation exactly, but basically he roams the land now punishing other 'Gary Oaks', seeing as how he does specifically go after Atty who he identifies as a Gary Oak, even with a speech about justice.
Could possibly be as atonement for being the original example of it, if coupled with the above WMG then this could be triggered by Ash's mysterious death.
- Alternatively . . .
The Masked Man is Ash.
If the disappearances are connected, then it may be possible that both bodies were never found. It's just assumed that both are dead. However, it may turn out that Gary really did die, and Ash is so consumed by guilt at failing to save him that he could never bring himself to return home (out of shame and out of fear of confronting Prof. Oak about what happened). He's spent the last ten years taking his anger and frustration out on whoever he deems to be an abusive trainer: trainers who couldn't care less about their Pokémon, who only want to use them for fighting, and who purposely target weakened or helpless trainers. Unfortunately, years of bitterness have hardened him to the point where he's not above completely devastating the Pokémon of Jerkass trainers.
As for where Pikachu could be in all of this . . . maybe Ash lost him, too?
The Masked Man is Daisy Oak.
Her brother and famous neighbor are missing, her grandfather's gone loopy... where else could she be?
We might find out more of the backstory when Atticus reaches Pewter City.
Unless the Gym leader has changed, Atticus will face Brock, who happens to be one of Ash's closest and oldest friends. There might a possibility that he could end up hinting at what happened with Ash and possibly Gary.
- Assuming this is actually in the anime universe and not just naming Red and Blue Ash and Gary, then Brock's borther Forrest is the Gym Leader.
Dragonthing's going to go through a very rebellious stage upon evolving.
Probably not to the level of "I SWEAR TO GOD WHEN I EVOLVE I'M GOING TO KILL YOU ALL", but enough that Atty's going to realize just how much he took DT's Undying Loyalty for granted.
The Masked Man is Gold
He has a Feraligatr, one of the Johto starters. But in Gold and Silver, when you reach Kanto, your Pokémon should be way more powerful than everyone else's. But the Kanto trainers are somehow level 50-ish. Obviously, if Gold really went to Kanto after beating the Champion, he would be about as powerful as the Masked Man seems to be.
Also: Black hair.
- It also goes well with the common game WMG about Ash/Red dying after he got beat on Mt. Silver. Gold accidentally pulled a Gary Oak in a dangerous spot and a life was lost because of it, that's why he was so pissed at Atticus.
Mokepon will become a Deconstruction of the Pokémon universe's society.
The ridiculousness of the Pokemon premise has been Lampshaded multiple times in the comic. However, Atticus has brought up the fact that this society seems to only emphasize careers involving pokemon, specifically pokemon battling, and that it seems to have little regard for any other aspirations people might have outside of pokemon. After a near fatal run in with Thaddeus and Trixibelle (Team Rocket members), Atticus becomes flabbergasted at the idea that children are the ones sent on these "journeys." It wouldn't surprise me if, by the end of the comic, Atticus ends up spear-heading a campaign to reform society in the Kanto region into something more reasonable and less pokemon-centric.