Pick a ship to build around and the rest will fall into place. For example if you build around Biggs, you are going to need target locks. That would be Vader's ship (I know others can target lock but vader is guranteed every turn and they dont wear off.) Biggs is going to perma taunt due to all the target locks so needs healing. That would be JC (two healing skills). How do you increase Biggs damage? He perma taunts so retribution is a huge boost for hm. So Maul is in. For the last slot we have several options. Ahsoka to dispell. Geo soldier to dmg and call assists. Wedge for damage, 5s for dmg due to his missile pod attack when vader TLs entire team. Or you could go for Boba. More TL, dmg output and two AoEs.
So this team would have biggs,vader,jc,maul and Boba. Which cap ship suits them best? Surprisingly Ackbar. He heals ships that attack out of turn and both this basic and AoE call assists. JC calls an assist and when biggs has retribution, he will gain tons of protection, probably more than the opposing team can strip away. His heal and cleanse skill can help any of your ships, but is best used to cleanse Biggs as needed. And finally, his ultimate allows double attacks. Two seismic charges in one turn...yes please.
Anyway, this is just one example. Pick one or two ships to build around and let the rest fall into place to support them. Synergy in fleet is a bit different to arena, as it is less faction dependant and more dependant on individual skills synergising across your fleet.