This might sound outlandish but I thought it might be pretty cool. I've been playing a lot of FTL lately and after starting a thread that turned into a (friendly and constructive) debate about Air Combat and it's merits in Xenonauts, I thought about boarding enemy UFO's.
It's a concept used in FTL to board enemy ships, dispatch the crew and basically come out with the maximum amount of salvageable equipment. So, I thought this would be a neat concept when the Xenonaut forces start to engage the larger ships. There's pretty much an infinite number of cool ideas you could use with this concept, one being storyline purposes. I also thought the risk of bringing your Chinook into a battle would be pretty tense. Or, you could even design a new, smaller craft for like a Squad of 6-8 or something specifically for boarding enemy UFO's.