In the past I went mostly by favorites, and would keep legendaries because it was cool. But when I got older I realized my teams became terribly imbalanced. Many of the Pokemon that I love enough to consider favorites are similar types, and although they are trained to be strong, one right opposing type can wipe them out. My Crystal party, albeit my love for them, wins the all-time award for weakest because it had TWO water and TWO flying and that made two thirds of my team, for lack of a better term, electrocuted to death. My other two types were electric and fire, which didn't do enough to balance my team out.
When I got Ruby version I started paying attention to variety. I needed to find a balanced party of different types that could easily back each other up if one was opposing something it was totally weak against. Some Pokemon I knew I'd keep right away--Taillow and Poochyena because they were just so darned cool :p--but otherwise from that, I was switching a lot in the first half of the game to get the most effective team I could. This led me to liking a lot of Pokemon I didn't pay attention to before. Testing out their abilities really made me appreciate how they can be used effectively, even Rattata. Makuhita seemed pretty weird when I first met her. Mawile, who I'd caught in the same location, seemed like a much better pick, but I decided to give Makuhita a chance because a fighting type was something I was looking for. It turned out to be one of the best choices I'd ever made in Pokemon. The rest of my party I cherished more, but Makuhita-Hariyama was an excellent member and she got me out of a lot of fixes. She's very underrated. She definitely made me forget about Mawile, who, for a while, I considered "cooler" for being a jaw-clamped Steel type.
Upon reaching the second half of the game, I had a pack of Pokemon that made up possibly my most favorite party that I'd ever had. By the time my game corrupted and reset every time I turned it on, I had Swampert, Swellow, Mightyena, Gardevoir, Hariyama and Lairon. They were amazing. <3 Even better, they taught me that variety really can be more favorable than preference. I've even looked up potentials online to check their types and movesets. In my Diamond version--the only handheld Pokemon game I have that doesn't reset automatically--I've been switching frantically, saying goodbye to a lot of cool folks, to make a good all-around team. Hoothoot-Noctowl I consider one of the very best and I totally blew it by to opportunize Pokemon I like way less. I even considered using Chansey for a while.
Still, though, I do have "stubborn picks." I ALWAYS have a bird Pokemon in my party, because I love birds and Flying is one of my favorite types. This is practically half the reason why I own a Staravia, part of the only bird chain I dislike--the other reason being it is a powerful fighter. And sometimes, my blatant dislike for a Pokemon bars me from ever giving it a chance. I don't care how powerful Ambipom is or how versatile Nosepass is with its TM and HM ability. I'm not using them. :|