The new commander menu has a few issues

1 mortar fire - the small map that now appears doesnt zoom in enough for accurate mortar fire. I'm assuming air support is similar, but haven't checked yet.
2 no option to garrison your own squad to outposts etc in the new menu (your own squad, not hc squads)
3 fast travel now only works to outposts and friendly towns - pain in the a** now I cant fast travel to watchposts and roadblocks
4 when trying to recruit units for your own squad at the flagpole at your home base, the game wont let you buy units unless you have enough player money - even though the cost is paid by the faction

Theres been some good improvements though, I noticed the enemy ai factions are now utilising boats more than they would have.