FinallyForged

I haven't tried the map editor before but I'll give it a go.
The NPCs are there primarily as a way of gaining rewards, so it's all down to implementing those rewards and the value they add to game-play.
Regarding the other point. There would be choke points that need defending with maybe some statues/orbs/wells and some simple ready build defenses that would need to be overcome to get to the base, naturally players can opt to bolster the defenses here.
The need for a teams defenses essentially all comes down to card selection, so I don't know how feasible it is to alter the pre-game interface so that all the team's cards are displayed on-screen for a quick overview to help make selection easier. Together with this feature also add a timer (say 3 minutes) for the team card selections, this is something that works well in other games.
You mention the character population and I do see that being an issue in this type of game, so is it possible for a character control limit of such as say 5 XL max for each player (with variation for a mixture of the other sizes)?
I guess what we're talking here is more or a new game mode than just a new map.