So that the optimal use of any fleetwide skill isn't to spam 20 Paragons.
I wouldn't do that to begin with. I don't do tryharding super optimal builds in a single player game, that's dumb.
Because, for example, when you get Special Modifications, you get 10-20 new opportunities to spend story points on ships. When you get Systems Expertise, you have no new incentive to spend story points on anything, so as a participation award story point sink, you get the elite upgrade.
You can also think of it this way: combat skills cost 1 1/4th of a skill point to fully unlock.
This would make sense if Industry also got a nice elite effect as a consolation prize, but it doesn't allow you to tap into comparable power. Only Combat and Technology get the good stuff either with or without elite effects, being vastly OP compared to Leadership and Industry.
Also, sorry for late reply.