I agree it would be nice for gills to actually be relevant at some point. The fact that it's prevented by pressure concerns is disappointing, now that you mention it.
Not needing the Depth Suit would be a huge advantage. It's not good for Techs and Smugglers and not all that great for Mercenaries, either.
There are no breathing concerns in the Queen of the Deep fight, either. What other places have water? The fishing hole on Uveto?
Two problems
1. There would have to be something to do underwater (or somewhere that could only be reached by going underwater).
2. You'd need some other way to achieve the same goal, since TFs aren't supposed to be mandatory. A 'Rebreather' Or SCUBA Accessory, maybe, or Airtight Armors.
There might be a problem with underutilized mechanics. Climbing Kit, for example. I'm waiting for more hazardous environments so the Shelter Drone might actually be worth it.