"He told himself that he didn't choose to stay home instead and train for 2 years for nothing."

Considering his pokemon are all L5, yes, I'd say he did stay home for nothing.

I'll give you credit for actually giving him pokemon, but if he's been training them, they should be higher level than that. You need some way of justifying that there was some reason or advantage to staying at home.

Also, dratini? No way. The houndour is excusable. The insanely rare, absurdly overused dragon type is not.

"He could play any major sport. You name it, he played it, but he was smart as well. In the 3 years of school, he got straight As and participated in many extra-curricular activities. When the day of graduation came, his outstanding grades earned him a choice between the three Kanto starters. He chose Bulbasaur.

Todd was also a master planner. He planned his day out and today was no exception. He planned his whole team, battle strategies (hence his ability to complete FF XI 3 times) everything."

NO. Is this in any way relevant to the story beyond you going "LOOK! My trainer is cool! And super awesome!"?

If he's a good strategist, we'll see it in his battles. If he's not, you've just set yourself up to fail as a writer. Saying he's intelligent rather than trying to write him as intelligent has the same issue.

"It is supposed to scan the real life battles and put them in Game Boy graphics (although if you ask Todd right now he'll probably ask "what's a Game Boy?")"

Also no. Don't break the fourth wall. If there are no gameboys in your world, then it will not show the battle in gameboy graphics and you can't describe it as such. It will show them in simplified graphics that, were we to visually see them, look similar to those of the gameboy in our world.

...his battle was not planning. It was just a mary-sue victory because you decided his L5 pokemon are absurdly powerful and unbeatable. Claiming credit for a victory that involved no actual planning as being because of his awesome plan is utterly idiotic, and serves to highlight what I was saying above regarding showing he has these abilities, rather than arbitrarily claiming they exist in defiance of all actual evidence in the story.