something I don't think many people realize is that several characters in media possess at least some Mary Sue-like traits. One thing that particularly gets to me is always arriving at the right place at the right time... of course, it's probably inevitable that this will happen at least once in any storyline, as chance happenings tend to move several stories along. That said, I'd be willing to let it slide if it occurs sparingly, and I'd especially be willing if they at least try to explain in a realistic fashion how these factors manage to come together at a particular place and time (as in NOT something along the lines of "Hey, I'm the top technological expert in the world and I happen to be walking through this forest that you're lost in, hundreds of miles away from civilization, for no particular reason. Come with me and I'll help make you stronger, 'cause I'm a nice guy and I take time out of my life to help any random sob that crosses my path").
As a whole, I'd say the Pocket Monsters franchise is just riddled with that type of flaw. First of all, there're the games. Now of course, as the player, there are gonna be several things put in the game meant to be accomplishable by you, but even so, it's hard to ignore several things. You're just some 10 year-old kid who just started raising Pokemon, so how come every random trainer you spot in the wild, some of whom look like they might have years of experience under their belt, are carrying around some weakass Pokemon about 10 or 20 levels lower than your's? And how about the way you always show up to stop whatever evil organization (they carry weak Pokemon themselves) from carrying out some scheme, and ultimately disband them, even though there should be several other people in the world easily more capable that logically should've arrived to stop them first. Don't get me started on how you're the first person to find a legendary Pokemon's dwelling, usually some cave or tower in plain site, and end up being the one to capture it.
Then there's the anime. Aside from the episodic nature of it all (how many weeks in a row can they stumble upon some town holding a festival or run into another random loser having trouble with their Pokemon?), there's no denying that Ash and the other characters have pulled through with some deus ex moments. The first season, in particular, seemed to be the worst offender of this... I mean, Kingler's evolution, anybody? How about Flint, who was supposedly standing at the entrance to Pewter City for years in hopes of finding a trainer to beat Takeshi (and why, pray-tell? I don't see how that's at allnecessary for him to come back home), only to finally find it in Ash? Or how about the way Ash managed to find all three starters, what are seemingly very rare Pokemon, consecutively (don't you just love the writers' BS with the way they were, and still are, always trying to whore those guys out? )? Even Team Rocket following him seems kinda unreasonable, and aside from comic relief, they've really only become tools for the characters to get into battles week after week to "try" to make the Pokemon's strength-building process a bit believable, even though that too has resulted in a load of crap at times [cough]Squirtle's Ice Beam[cough].
I'd be willing to say Pikachu itself is a huge deus ex, though really, I wonder if it's anywhere near as strong as Team Rocket make it out to be (it did first discharge electricity at them while being powered by a bike). Plus, even if it is extraordinary, Professor Oak was hesitant to give it to Ash in the first place, and it was disobedient for a brief while (and it's not like being extraordinary helped any against Richie, who is without doubt one of the worst, poorly conceived, Gary-Stuish characters in the whole anime). Though, I can say that all these "work together/trust me/we should respect Pokemon" moments with it and Ash lead to a bunch of BS (must anime writers always make partnerships seem cheesy as hell? ).