A) 1-allow only official discovery player factions to use capital ships (to reflect that it takes more than one person to aquire the materials for such a ship.) 2-limit the number of capital ships each faction can own at any one time, (that way a faction would only choose its best and most active players for those slots.)
or
B)Make capital ships so prohibitively expensive that it would take only a strong faction with member support to aquire one. Picture 5 or 6 active trading characters trading consistently for 1 or 2 months before they have enough cash for a battleship and you'll get what I'm seeing. This would mean that only good charismatic faction leaders with the necessary organizational skills and member support would be able to get a battleship rather than any random unaffiliated loner.
Perhaps too strong a pill to swallow for some of us, but either of those two options would ensure that fighters always outnumber capital ships. It would make trade and commerce between factions more important, as well as diplomacy.