Shane doesn't have a Dratini, does he? Dratini
is relatively common as far as starters go, but you can justify it easily, considering that his final evolution totally kicks ass and is therefore a better Pokemon to journey with than, say, Rattata.
This is actually why it's probably not a good idea to start out with a Dratini. (Incidentally, it's not really a common starter in fanfiction, as I can't name an OT story that has a trainer start with one -- and, yes, I've read a
lot of OT story beginnings. Yes, I know a number of OT RPGs have Dratini as an option, but not all of them do. Likewise, OT fanfiction isn't exactly the same as OT RPGs.) First off, it's rare. Famously so. As in, in certain 'dex entries (RBY and LG, and DP calls it a "Mythical Pokémon," caps and all), it's mentioned that Dratini was a mythical Pokémon whose existence was even debatable before a colony of them was discovered.
Second, yes, its evolution is epically strong (literally), which means you'll be relying completely on its brute force to have the character win every battle.
Third, what's wrong with starting with a Rattata? A good author can ignore the common cry that it's weak (which, seriously, the Fangs alone are pretty decent on a Raticate, and have we really forgotten F.E.A.R?) and turn a supposed downfall into a major plus for the character. After all, if you see a Dragonite beating the crap out of entire teams at a tournament, for example, it's just not that surprising because Dragonite is normally thought to be able to hold its own. However,
Raticate takes cleverness on the author's part -- a sort of creativity that allows the author to think outside the box. You just can't rely on brute strength to win if you're going to use a common or otherwise "weak" Pokémon like Raticate. You have to combine moves or use moves in new ways -- like having Raticate Quick Attack to behind the Dragonite, up the back, and to the wings, where the Raticate Crunches them off because they might be an Achilles' heel for that particular dragon. Not exactly the direct approach of "HYPER BEAM TO THE FACE." In fact, it might even be seen as low. Yet, at the same time, it's a bit more interesting because not only is it more complex than just your standard Kamehameha battle but also because there's a very real risk that this kind of thing would really screw up for the user. In other words, it's extremely unpredictable, and readers tend to like unpredictable. (Or, at least, that's what I've been consistently told by reviewers.)
Short of it is that just because it's stronger doesn't mean that it's a better choice for a starter. You're not trying to win the game, after all. You're trying to forge an interesting story, and to do that, you'll have to add as many obstacles as possible to force the characters to overcome in clever ways. One way to do that is to go for the Pokémon that
isn't notoriously a powerhouse.
'Course, this all is a moot point because it's implied that the OP isn't asking about which starter to use. I will say, though, that the Rocket Game Corner offers several other interesting choices for Pokémon that either are rare or are called rare by the games, ranging from Porygon to Clefairy, and if he chooses something that isn't Eevee or Dratini, he's got some pretty flipping awesome choices left.
I have to say, though, that I agree that I'm wondering about how Shane will fit into this picture. I get the vibe that this is an OT story in which he goes off to investigate what's going on with the birds, only to find himself hitting one surprise plot after another ("Evil team is using the birds, so I must help stop them! ...Oh wait, no, they aren't! Oh noes!"), but on the other hand, it sounds as if Shane's taking more of a background role. As in, he doesn't even really encounter the legendaries themselves that often, and I wonder if that means his story's not going to cross with the other story that often either.
Other than that, the idea of a legendary group actually actively using humans for a sinister purpose is an interesting concept that could actually work if the one pulling the strings isn't stereotypically evil. (Lulz, psycho Mewtwo.) I'd just really think about how the human characters come into play in all of this.