Flight-capable wings do allow Steele to fly, in specific instances:
1. Zil fly up to/down from their village without issue, and so can Steele, if they have wings. 5 Energy to ascend the waterfall, 0 to descend.
2. Myrellion's Deep Caves: 5 Energy to descend, 25 to ascend.
3. There's an out-of-the-way cave on Uveto that Steele can fly into and out of.
(These uses are also much faster in in-game time, if that matters.)
4. There's a quest on Myrellion that allows Steele to sneak into a location if they have wings.
5. Zheng Shi's Shock Hopper automatically does damage over time unless Steele has wings.
6. When running away from combat with wings, the text has Steele flying away. (And I think it does increase escape chance.)
Tossing some ideas out there:
At the moment, there are 4 enemies I know of who fly.
1. Zil Males. They're level 1, so they're quickly rendered a non-threat.
2. The Storm Lancer random encounter. He can be shot down, but it gives him a buff. I've got a melee Tech Specialist with 25 Aim who can hit his Jetpack pretty consistently. Of course, Tech Specialists get a bonus to accuracy based on Intelligence, so that may not apply to everyone.
3. The Storm Lancer Valkyrie at the outpost. She can be brought down with an EMP or ranged Stun, according to the Wiki.
4. Overseer Maike. This one is annoying because she completely regains her shields when she activates her flight and starts spamming Lust attacks. (Compounded by the fact the player doesn't really have many good ways to get Lust defense.) She's technically optional.
Am I missing any?
Of course, if the Storm Lancers can have jetpacks that allows them to fly, why can't we? Why can't we follow Overseer Maike, when she flies up to a rock in the cavern? (Game balance issues aside, obviously.)
Current counters to Flying:
1. Ranged weapons. You have them for a reason. On the other hand, each class can specialize in ranged or melee, and being forced to use the other drastically decreases damage dealt. Are there any ranged shut-downs? (Blind maybe.)
2. Special Attacks. Grenades, Thermal/Gravidic Disruptor, etc.. These do damage based on your stats, and can't be upgraded via gear. They also require Energy to use.
3. Mercenaries can choose Lunge at level 10, which allows their melee attacks to hit flying enemies. No special attack needed, no energy expenditure. It also adds a stagger chance against non-flying enemies and also works with Second Attack.
If flying enemies become more common, I'd handle it like Uveto. I.e, having multiple solutions available for different characters. In addition to wings, have a Jetpack for the accessory slot and maybe an armor. We already have Daedalus Threads, why not Icarus Threads? Maybe have them grant a special attack that allows you make one (two if you have Second Attack) attacks with your perks against flying enemies for some amount of Energy.