While most people enjoy being over-leveled for things such as the gyms, the elite four, and the legend matches, I enjoy being under-leveled. I enjoy the challenge it provides.
I also assign one pokemon each to take on the gyms. While the pokemon I use the destroy that gym may not make it into my final six, they'll be adequately trained and remembered as the one who destroyed a certain gym.
I make sure to always have variety, I can't have two of the same type on my team. This only applies to their primary type however, so I could have a Water/Ground type, and have a Ground/Rock type on the same team.
I don't have legendaries on my team. I simply don't allow it, I like to feel like the average trainer, not some suped up destroyer of worlds. The average trainer (most) never walked around sending out their Darkrai's or their Suicune's, it just doesn't happen.
Pokemon have to be a specific gender depending on how they look. For instance, I would never have a male Gardevoir, or a female Haxorus, it just seems odd to me. If a pokemon looks male, I make sure to catch/breed a male one. If it looks female, I make sure to do the same.
My lead Pokemon is always female, don't ask why, it's just what I've always done.
The very game I get is ALWAYS opposite to that of my real life rival, my best friend. While we both inevitably get the "third" version, we always get opposite versions ever since Ruby/Sapphire.
I had Sapphire, Diamond and White. He had Ruby, Pearl and Black. This helps us get pokemon we couldn't otherwise, content and such, and feel a little different.
I don't ride the bike. UNLESS I'm trying to move somewhere quickly and don't have fly yet. I like to experience the story on foot, Ash and pals never rode around on bikes (Misty's bike excluded), they made that long journey on foot. I like to look around and admire the surroundings and such at my own pace.
Like with the female leader pokemon, my trainer is always female. This usually equates to any game that allows me to pick gender. I look at it this way, who's bum would I rather be staring at four hours and hours while I play? The girls, of course.
I talk to myself as I play. No really, I comment to myself about the situation, the characters, the plot, and everything.
I train a little bit and do some sidequests before each gym, makes the game feel a little longer I guess.
Can't really think of any others right now...although I'm sure there are tons more.