We've played each scenario once now, and two of them we found to be really quite easy (Azathoth and Umordhoth), so I was thinking about how to change the Mythos cup to not only make the game a bit harder but also in a way that was thematic to each Ancient One (it's also a bit of a disappointment to me that each AO has the exact same Mythos cup distribution).
So I came up with this, which is to replace one of the blank tokens in the Mythos cup with a token depending on which AO you're facing:
Azathoth - Doom
Umordhoth - Monster
Yog-Sothoth - Headline (build the Headline deck using 20 cards instead of 13)
Cthulhu - Reckoning
Unfortunately, the game doesn't come with enough tokens to actually implement this, so instead just say that the first blank token pulled out of the bag after each time it is refilled is the required token.
How about maybe replacing the purely random set-up of the Headline deck with a partially random set-up? To make the easy scenarios harder, say 3 of the harder Headline cards could be pre-selected and only 10 are random. Or would this make things too predictable?
On a related note, one small gripe I have about the Headline cards is I'd have liked a few specific to each scenario. Having the King in Yellow play pop up randomly is for me a little bit lame.