I like to use Charizard, because he is my favorite Pokemon, but I know if I say or type that where older Pokemon players can see it, I'll get b******d at about why using him is akin to me spitting in their eye because he SUKS and STEALTH ROCK.
I also like to use Pikachu, because, again, he's one of my favorite Pokemon. Is he the best? Hell no. Is it fun to play through the game with one? to me, yes.
I could name 20 more Pokemon I use regularly that everyone here could list 10 or more reasons why I shouldn't ever, ever, EVER!!@*#@^#@ be using them.
I have to think there are other people who play with their favorites rather then the best, but every board I visit just shows people using only top tier Pokemon.
Do you play competitively? That'd answer your question right there. If yes, then of course most people are gonna use the highest tier Pokemon. If your favorites are low tiers, stick to the lower tiers.
There's nothing wrong with using your favorites, of course, but you should expect to see a lot of the same faces in pvp. I tend to stick to singleplayer mostly for this reason, so I can use the monsters I find interesting in any given run.
I don't use only my favorites, but I'll still use my favorites. My two favorite Pokemon are Medicham and Victreebel, so I use them on a sun team, since Victreebel is much faster under sunlight. I don't like Ninetales that much, but it's the only non-Groudon Drought user, so I'm stuck with it.