I don't remember what team I used for the beginning of the game when it first came out, but I know Magus went in right after he joined.
On my last playthrough.. Crono, Marle and Frog were my team for the first half of the game. Crono, because he was mandatory. Marle and Frog for their healing, Frog's physical damage, and a few good double techs between them.
After Zeal, it was Magus, Crono and Marle. Crono's had great physical damage when you gave him the rainbow, and it took a lot to kill him. Magus, because he's awesome and his magic absolutely trumped evevryone else's attacks. Marle was still useful for her healing and Haste spells, or using Elixers every turn while fighting Zeal on top of the Omen.
This is for a non-plus game. With these teams I didn't die once, and got to level 50-something at the end in a single run. I never took the time to get to level 99, so Luminaire was never quite as effective as Dark Matter. It's more fun when the mage deals more magic damage than the fighters, anyway.