There's been some confusion and disagreement about the portrayal of Gengar recently, so I would like to explain why things in this story are as they are.
TL;DR: Skip unless you want to see a bunch of stuff about Gengar and obscure game mechanics
Everything in VF is based on something in a game, or an anime episode, or something somewhere in the Pokéverse, even if it's something very small and throwaway. This is not to say that our take on it is the only correct one, because there are as many opinions as there are Pokemon fans, and nobody's idea is necessarily wrong! However, I do want to show that none of our story choices are arbitrary--everything we've done has something behind it--and I am happy to explain our reasoning at any time if people want to know.
Let's look at the Shadow Pokemon thing, because it's a good example of how the VF writing process works.
- Shadow Pokemon in Colo/XD have curious parallels with the Dark Ball controlled Pokemon in the Celebi anime (in Japanese version of Colo/XD Shadow Pokemon are in fact called Dark Pokemon) and with Blake Hall's Shadow Crystal plot in Ranger: Shadows of Almia.
- There is a Darkrai as a major element in Ranger, and a Darkrai as a major element in Time/Darkness.
- Ranger is set in a region where human presence is limited; PMD is set in a region where humans are nonexistent but strongly hinted at being present in the past, through architectural elements (see: friend areas) and found items.
- In Ranger, Darkrai is seen to lose control during battle and enter a furious aggressive state, just as Shadow Pokemon do when in Hyper/Reverse mode.
- In Time/Darkness, Darkrai is malevolent, but is restored to a former state of innocence when Palkia defeats him; in Colosseum Shadow Pokemon are "purified" through battling, although not fully cured without the intervention of Celebi...
- ...which brings us back to the Celebi anime.
When we put all these things together, we found that they could be made to tell a new hidden story that ran underneath the others throughout several years of the Pokemon media. This story is what gave birth to PMD:VF!
So, let's take a look at what's going on with Gengar.
In Sinister Woods, your team of two was able to defeat his equally leveled team of three with two of their members being fully evolved. A level 15 eevee or bulbasaur shouldn't be able to beat a lv16 gengar up no matter how you look at it. The Meanies were nerfed! Our conclusion: Gengar is not fighting optimally. This is a game thing--of course the game designers wouldn't want a battle to be unwinnable--but it's not the only example of weird battle behavior on Gengar's part.
Later on, Team Meanies admit onscreen that they are only Normal Rank. Given that they are fielding, again, a fully evolved Gengar, that seems very strange. Lv1 stats alone suggest that he ought to have been able to roflstomp any Tiny Woods tier mission SOLO (he's either immune to or resists everything in there), and he's been confirmed to be at least lv16 from the Sinister Woods battle (see: Night Shade). Our conclusion: Gengar is not making appropriate use of his species abilities.
Later still comes the Mt. Freeze escort mission where Gengar is unaccountably given the moveset Leer/Scratch/Quick Attack, two of which moves he is incapable of learning under any circumstances. Now, every NPC is de-leveled to 1 for escort missions, but at level 1 Gengar SHOULD have known Hypnosis/Leer/Spite. Perhaps the game designers felt that his spamming Hypnosis would have made things too easy. Our conclusion: Gengar is using inappropriate moves for his species.
Finally, there's the general thing in PMD where ghosts can be hit by the basic push attack. This was probably done so you don't get walled by unkillable Shedinja, and it's not unique to Gengar, but it is worth remembering that under PMD rules, yes you can smack Gengar round the head. :3c
OK, this is gamist stuff, but it's still observed behavior, and it can be read in some interesting ways. The conclusion VF drew is that Gengar doesn't fight like other Gengars. While normal Pokemon may be limited to the "moves" they've learned, he still thinks like a human and the result is that Gengar breaks the system. In his mind: Gengars don't learn sand-attack? What's to stop him grabbing a handful of sand off the ground? Gengars don't learn scratch? He's got fingers, right? The result is that many Pokemon will find themselves getting a bit flustered when they face him, because he can and will do the exact opposite of what's expected. When you're braced for a Shadow Ball, it can be off-putting to get punched in the face!
However, his methods have downsides, as Kecleon is about to explain...