Great topic! Its not jumping the gun to get constructive convo going.
TFTD had known flaws for numerous reasons that went to production. Thats why the strat guide varied from the actual game. I'm not complaining mind you...glad they did because the game would have been obsolete on arrival within a two years.
Deep Ones are based on HP Lovecraft, and clearly the creative image of the Deep One with a rifle is based on that and other authors lore. XCOM is a game of discovery of lore, and the real threat behind them. The one in game does not reflect the lore of Deep Ones.
That being said, Deep Ones were supposed to be hybrid. They were swift, moved on all fours sometimes and struck with their claws. They could also move on their legs, but stand like a man. They should not have a spit attack, but should have a viscious claw attack, or a weapon attack with their sonic weapons. IMO, Deep Ones, if implemented, should be segmented into "classes" if you will like Sectoids.
IMO, they would be:
HYBRIDs and MONSTEROUS.
MONSTEROUS (or whatever) should be based on a Reaper. Move fast, deliver a nasty melee attack, but unlike a reaper, can go through doors and climb stairs!
HYBRID: Should deploy weapons, have intelligence, and unlock lots of key lore.
In theory, they are not aliens...or descendents of aliens. They are terran. I prefer to think they were subjugated by the aliens, and with aliens deep asleep, the deep ones escaped and bred into quite oceanic cities. For the past few thousand years they endured, but kept quiet, for fear of awakening the Alien/Gods.
Hybids are actually the children of Man and Deep Ones, since times of old. Deep Ones have low reproductive abilities and use human reproduction through women sacrificed to gods of the Seas, etc. (Deep Ones had no cloning technology...they had lost all connection with technology upon escaping their masters 10 millenia ago.
At birth, Hybrids appear as children who love the call of the sea. They look and appear as human in every way. They just feel an uncanny affinity for the deep ocean's call. As these children get older they grow into their true lineage (oily scaly skin, rheumatic eyes, horrid teeth, bi-sected tongue, etc. ) Eventually they get the call of the wild and throw themselves to the sea where they metaporhosis over decades into Deep Ones. They wander the deep in search of others of their ilk. Meanwhile they are witnessed by sea-farers as mermen and mermaids.
Eventually they formed cities..ancient cities. Devil's Reef, Ahu-Y'hloa, G'll-Hoo, Bod Reef, Bermuda, etc. Quietly and simply they lived...always in balance with their environment.
When mankind began to travel beneath the waves in early 20th century in their loud machines (Submarines), the Deep Ones tried to warn mankind not to tread beneath the waves and disturb the ancient Gods sleep. They're requests became demands, and their demands fell on unsympathetic human ears. The Deep Ones warnings eventually threatened the tide of mankinds progression to conquer earth, sea, and sky.
The US gov't fought a secret oceanic war against these underwater cities with their submarines, torpedoes, and depth charges... and destroyed Deep One cities in the late 1920's and 1930's. It was near genocide, and America covered up the entire affair like they would one day do in Roswell. When the ancient ones eventually awoke (i.e. TFTD), the Deep Ones that survived pledged themselves to their old masters in fear...Their "masters" used the Deep Ones to find out about mankind, and used the Deep Ones in their scheme to take the earth as harbringers of ruin.
Interestingly...upon interogation, Deep Ones are free from the evil influences become sympathetic. They offer up a bounty of lore and technology they gleaned from their masters in order to help mankind, whom they see as more brother and kin.