Here's an idea to consider - because FS capships are so large, you might consider a mat-type vessel which you can have turret and subsystem tokens on? You'd besically unroll a vynil ship mat from a tube and lay it across the table. If you fly across a ship when attacking it (fighters and bombers can fly across the ship mat), you'd have to roll to check for collisions (kind of like WH40K when ending your vehicle move over a forest). The capship doesn't move, but this doesn't really hurt an FS boardgame at all as big ships tend to be more story pieces than anything else.
...If you want capship miniatures, the smart thing to do would be to keep the fighter miniatures and adopt a new ruleset which turns the fighter pieces into squadrons. Then you could have scale ships which can maneuver across the table, etc. Same game pieces, new cards, and you let the players play the games/story the way they want to.
