As someone who does routinely mix Lovecraft with Traveller...I really am looking forward to this setting.
However, it can be done right, for instance substituting the Ancients for the Great Old Ones - as a racial memory - as psionic imprintur across the millennium that is perpetuated by memes. Over time, these get distorted into classic Good/Evil divides till we arrive at the Milieu in Traveller that you call home.
Therefore, these become Monsters of the ID that may actually have their physical presence with the advancement of science - through the creation of artificial life or terrible constructions (ie the creation of bioweapon that is taken the genetic characteristics of thousands of lifeforms across chartered space or a runaway mini singularity). While these scientists are not sorcerers (although a more primitive culture would perceive them as such) and are not mad/insane in the conventional sense but certainly are breaking the frontiers of normality.
Add to that all the nastiness that universe constantly creates whether it be child slavery to serial killers. Those people may be cured in the ZC but not the Imperium. Some might be even found among the Nobility or CEOs or the Megacorporations - imagine what all that power and resources can do - to people who are not accountable to anyone.
Then there is just the plain weirdness that is already out there. We cannot judge Chartered Space from the vantage point of 21st Century Terra. Interaction with alien species, environments is going to create lots of weird new things.
Then there is that abandoned mining colony on the outer fringes of the system. When the players arrive. There is blood everywhere smeared on the wall, garbled messages in the log. Exploration of the mine reveals a fresh tunnel leading down away from the ore's vein.
All this is classic Traveller scenarios or Cthulhu take your pick. Convinced, you [FONT=arial,helvetica]
aramis? Take another look.
Also, a great resource for Cthulhu/Traveller crossover with appropriate serial numbers filed off or changed (as there is a wealth of scenarios) is the website for Cthulhu Rising (http://www.cthulhurising.co.uk/downloads.php)
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