I think a soft fix for the time being, before a proper look at it can be done, would be reducing the HP of the enemy Leaders by 20-40% to begin with. They are durable beyond the sensible, and its a kick in the teeth having bunch of your tanks hammering on the boss, doing ridiculously small damage (and we are not talking about weak tanks at all, with their dmg skill active), and the enemy spawning one or the two of the broken ones and then wiping the floor with you.
Also it seems the enemy commanders do not operate under the same rules as we do. They either do not have to adhere to the point limit or do not need to wait for their points to be refilled before deploying another tank.
We can see this for example when you deploy two tanks each costing 4 points, the enemy deploys their, they wipe you out and by the time they are murdering your squishy leader the enemy spawns another two, while you dont even have enough for another 3 points one.
While this would not fix the broken combinations it would certainly alleviate certain amount of hardship as, you might be able to take down the leader before the wombo combo spawns, or they could not keep pumping out multiple expensive tanks while you are still waiting to refill the points for one.