well, you shouldn't be able to command from a small and maneuverable ship front line ship, just like you shouldn't have a small and maneuverable ship with 10 Plasma Cannons, no matter how fun that would be.
You should perhaps try to use examples which cover analogous situations. A small and maneuverable ship with 10 Plasma Cannons which is actually able to make use of those 10 Plasma Cannons has a significant advantage over anything currently in the game, except maybe the Hyperion. A small ship with command capacity equaling that of a large ship is neither advantaged nor disadvantaged; it's simply more fun for those of us who like piloting the little ships.
It's also not clear to me that the fleets in Starsector act as sufficiently well-coordinated units that the realism card really applies; by and large, ships seem to operate independently of one another, aware of what the other vessels in the fleet are doing only to the point of (mostly) avoiding collisions and friendly fire, but not really cooperating with one another, and you're very limited in your ability to issue orders to the fleet (and those orders are moreover somewhat loosely followed). This doesn't seem particularly indicative of a highly-trained command team with access to sophisticated command and control technology.
I also have a further objection on the grounds of fun. I like flying the little ships, I don't like flying the big ships, and I like bringing large fleets into battles. I don't support suggestions which penalize me for (trying to) having fun when there's no significant game balance issue in play (and for single-player games, I am of the opinion that game balance takes a backseat to fun anyways, unless it's a fairly egregious issue).
Also, a comment: there's nothing currently in the game that says that John Smith's skills, as listed on John Smith's character sheet, actually represent John Smith's personal skills rather than an ability to find the right person for the job. Maybe John Smith isn't a fleet commander, but he's managed to convince Horatio Nelson to lead his fleet in battle. Maybe John Smith isn't a great pilot, but he's good friends with Manfred von Richthofen, and the Red Baron has agreed to fly Smith's personal ship in each battle while Horatio Nelson commands the fleet from the fleet's flagship rather than your personal flagship. Maybe John Smith isn't that good with technical skills, but he's managed to convince Thomas Edison, Alexander Graham Bell, and Nikola Tesla to head up the fleet's technical and engineering staff. Maybe John Smith isn't that good with finance and industry, but he's convinced his brother Adam and his college roomate Henry Ford to manage that side of the business for him. John Smith "has" all these skills, because he's managed to pull together a team of people who have all these skills, and he's managed to make them work together effectively. There's historical precedent for such arrangements, and regardless it's not like it's realistic for our avatar to be the ideal Renaissance man, with great technical skills, leadership skills, industrial and financial skills, piloting skills, etc which he can use simultaneously. Much of the Combat tree may simply represent how well your avatar chooses the crew of his personal flagship (at the very least, I'm clearly not personally involved in damage control at the same time that I'm manning the ship's helm, and I'm probably not also simultaneously crewing the guns or personally ensuring that the engines and power plant are running smoothly), much of the Leadership tree may represent how well your avatar chooses the command staff of his fleet, much of the Technology tree may represent how open your avatar is to the good ideas of his subordinates and how well he chooses those subordinates.