I havent played SMRPG in a while, but as i remember I used All of them equally. Im the kind of player who uses all characters given, not just a "power" team. Take Crono Cross for example, Ive beaten the game with the majority of the characters. Anyhow, My favorite team is Mario, Geno and Mallow simply because poor Geno and Mallow are seen only in this one game and I felt they could have been carried over into other games. But favoritism aside the most practical team IMO is Mario, Peach and Bowser. SMRPG had like no element of difficulty to me, and how I power-up. So, having 2 bashers and a healer works the best. And like stated earlier, Peach with the frying pan and boosted FP makes her too good to pass up.
This is one game I wish they'd make more like. They give only a few characters and ALL are usable and great. In addition to that, we all knew going in the main character. I was only dissapointed in the fact Luigi couldn't have gotten off of his lazy bum to help.