This weekend I was looking into creating a couple of decks after a longer hiatus.

One thing I noticed is an amazing lack of effects that work on subtypes. I wonder what they're all for since they're so rarely used.

A couple I've seen used: Deep One, Spell, Cultist, Monster, Investigator, Ancient One, and a couple of new ones: Zoog, Gug, Dreamer, Dreamlands.

But that's about it. Have they been used more often in the CCG?

yes much more in the ccg, allthough some are new to the lcg so in that case no, but im sure as this game gets older it will have a bigger card base and better/more cards that use them more

But there a a good number of subtype dead ends too, even with a boost card. The exception would be the strong deck based on a subtype.

Well, they did mention that the Deep Ones and the Mi-go will get some love in the Secrets of Arkham Expansion. I hope that the other factions get some as well (Criminals, Government, Scientist and what-not).

Alien Excavation (+4 skill) is the one Mi-Go boost card versus a few Deep One boosts.