My idea is that you can choose certain territories in the scenario which get a defence boost.

Also there could be a card that gives this. Now you'll have to use an emergency blockade for this but this leaves big neutral stacks if it's not attacked enough. I think a card that gives a defence boost on one territory for one turn is a good alternative especially in diplo games.

I have another idea with this for commerce games. This is that instead of cities you can also build a max amount of fortifications per territory that increase defence.

Going on the topic of features for diplo games, they are rarely useful for general WZ, and more often than not a user-made mod is used to achieve the requested function(s).

It would be nice if mods could add custom cards to a game tho...

I think that they can all be useful in general, except for choosing territories that get a boost maybe. Though ffa's usually don't use commerce and big neutral stacks are less a problem there.

It should rather easy to make a fortress or capital setting like the commander, just unmovable.

You loose the game if the commander gets killed. Also the commander just counts as extra armies, he does not give you better kill ratios. So not exactly the same. I know, i am a member...