I tend to perform best with Ivysaur. Both my Squirtle and Charizard still need a bit more practice, but I'm getting better at them. In actual application though, I try to use all three of them, but their rate of use depends on the current situation.
A good example is some matches I had with a Jigglypuff yesterday. Not being used to fighting a decent Jigglypuff, I had some trouble at first, but after awhile I felt Ivysaur had the best chance at racking up Jigglypuff's damage and scoring a KO. Since they like to be aerial, I threw ground and short-hopped Razor Leafs to keep them on their toes, and I used BAir and FTilts to keep them even more at bay (now that I think about it, I tend to forget I have UTilt and DTilt....). Ivysaur's good smashes are slow, but still they tend to work.
After Ivysaur, Charizard performed decently. While he has the strength to take out a Jigglypuff, her manueverability and priority made it tough for Charizard to really take advantage of power. His low speed didn't help either. But with moves like Flamethrower, he still made for a rather even match up.
I found it toughest using Squirtle against Jigglypuff. The way you use his aerials are rather similar to Jigglypuff, but it's his lack of attack range and slow smashes that made it really tough to use properly against an equally small opponent who could maneuver in and out of danger constantly. Shellshifting mindgames would help occasionally, but in the long run, he would best be used as a stall to get away or give time for Ivysaur to recover its stamina (in the event Charizard got knocked out early).
Now all of that's regarding Jigglypuff. The strategy of using the right pokemon would change depending on a different character. If a rather large or tall character that didn't have a sword, I would probably get Squirtle. For smaller or midsized characters, I'd probably stick to Charizard. For well-ranged or projectile characters, Ivysaur would most likely fit. It's about experience though, and it's also realizing that one pokemon just can't do it all....unless their opponent sucks.