You all seem to be missing the fact you are only talking about top tier players attacking command ships, and only a few ship classes at that.
What about the unfair matches where a squad of 4+ squad members at lvl 50 are part of a team that is fighting a team with only one lvl50 player? Making the CS even more difficult to kill would mean the team at the serious disadantage would be even more so.
Specially if you level the CS ships to match the players skill level, that would make it even more difficult for T3 ships to kill the CS, while giving the unfair match stronger team a huge giant advantage.
If you don't want your CS taken out fast, then protect it better. I have played plenty of matches where the opposing team simply bubbles their CS, and all players are healing or protecting their CS, but do not attack the other teams CS at all, the entire game, and they win.
Sounds like a lot of people want a strong CS so they don't have to worry about it, and can focus on killing the other team, in that case there are specific battles you can play without a CS ship at all. I would suggest you play those games and not Onslought.
The CS is good as is, perfect, you can choose to protect CS, or not and attack the other teams or split tactics, whatever you want. But it's part of the dynamics of the game that you have a ship that has more HP than any other ship in the game, but is vulnerable enough to force you to either abandon it, protect it, or split tactics which makes the game far more interesting than a better tanked CS that is so difficult to kill that you ignore it. That would do absolutely nothing for game mechanics nor tactics. It reduces the pressure and stress and makes it more lazy a game.
If anything I think maybe the CS ships field should keep you at a slightly further distance, so you cannot get right up on it. But other than that, making it stronger will make more people ignore it more often, which makes it an ineffective game mechanic for increasing strategy, game mechanics, tactics, etc.