Off with the biggest issue, Flak Gun unit use WAY too much ammo, heavy tanks fuel logistics looks like a minor issue with this. They use 60/30 ammo, so if you were to add 1(10x) unit into your troops, the heavy grenadiers would go from wanting 70 ammo stockpile into 800+(while having artillery would make it 180~). Battlegroup with 100 heavy tanks, 50 armored transport and 50 Flak would want stockpile of 2000 fuel and 3260 ammo. The fuel I can understand but the ammo not so much... it has to be mistake?
2nd
Now with custom formations you can consider adding some arty units into formation, but they cripple the movement of the unit entirely, adding 10 artillery into 1000 foot soldiers should not cripple them so much, it seems to be better idea to add Mech.Artillery instead(as you dont need to spent more points on formation and apc cost would be almost the same), which turns normal artillery more pointless, was hoping custom formations would make them more used in my games but meh, seems like no

3rd
Custom formation cost, it currently cost as much to add 1 unit to formation as it does 4, could there be option to add something into formation like you do now OR pay less for minor change or perhaps add multiple types but with less max amount. Also if you want to add artillery or something similar, option to add something to tow it, instead of having to spend even more planning points to fix the issue.
4th
You start to auto scrap cards when there are too many, could there be some list where you could add cards that always get scrapped instead of manually going trough them? When minors are gone from the game one does not really need the cards anymore etc.