Of course the idea is a disaster in terms of balancing but imagine a system like this:
You have 10 points for each commander.
Each ability costs points.
'Better' abilities cost more.
So for example a Tiger Ace costs 5-6 points, then you have to fill the rest with 4 abilities that cost 1 point. So you take tiger ace with smoke barrage or something like that. This would prevent accusing the system.
This right here. This is the only way custom commanders have a shot at being balanced.