Stupid nitpick complaint that is easily solved
I don't have my copy at hand, but some of the NPC stats seemed out of whack. Lots of high INT scores, as I recall, to the point where this random Deep One hybrid island has a seriously disproportionate number of people with above average IQs running around, to the point that the question is "why do they not have their own physics department?" Taking 3d6 as the norm for INT (2d6+6 results in a really weird curve where anyone top 2% or higher fits into 18, but that would mean compressing "very smart but not uncommonly so" and "one-in-a-million genius" into one score, whereas the curve for 3d6 has the top 2% at 17 and the top 0.5% at 18, which still requires some compression, but only at the point where IRL IQ tests start to break down; I prefer to think that 2d6+6 is just to ensure that PCs are smarter than the average bear) a 16 is top 5%, roughly - which would equate to an IQ in the mid-120s with an SD of 15.
This problem recurs across CoC sourcebooks: how smart a character is described as being often has little relation to their INT stat. Conversely, sometimes you see NPCs who are not described as being intelligent statted out with IQs that would put them in the top I may of course be misremembering in the context of Targets of Opportunity but in general this is something that annoys me. The obvious solution: adjust INT scores by comparing the curve for 3d6 to the curve for IQ.
Actual good opinion
I'm not sure how I feel about Black Cod Island. The background is cool. It's cool to have a potential foe that mostly just wants to be left alone. If your PCs are self-aware and relatively mature, "why exactly are we fighting these guys?" is an interesting moral dilemma. Delta Green was created to fight Deep Ones, but that was in another time and place.
However, it's hard to introduce into a campaign, and if your players aren't self-aware and mature, "we have to wipe out this entire island of indigenous people" can be an easy result. Gaming sessions where you find out who in your group of friends thinks genocide is a good idea are always unpleasant.