Thanks for playing!
When the enemy equips your crew, the currently worn items are lost. Could we get the chance to loot them back after winning vs. the current enemy team, so hard to come by items can be reaquired, sacrificing a loot slot for it?
Any worn items are returned to you at the end of the dungeon, you'll see them pop up at the guild inventory. Though there were some bugs with that in versions before Alpha 2.5.
I'll take your suggestions into account, but I don't want the grapples to be too strong. Though a boss is planned that will do exactly as your second suggestion.