Bastila Jedi with Yoda make GW a joke up until you can sim it. They don't lose effectiveness like Phoenix did. Palpatine Empire team is the same way, though a zeta Bastila team will shut them down. Best thing to do is try to bring your secondary teams up to par with your top team. Then on the opening battles of GW, switch teams on the first few nodes to give them all a turn meter advantage.
The clones though are a high value bang for the buck as far as how powerful they are. Galactic War determines your opponents based on the power of the top 5 characters on your roster. Regardless of if they have ever worked together or what. So if you keep focusing on one team, you will eventually run into its counter in Galactic War. Phoenix is countered by almost all teams with synergy if the power levels are similar.