Let me put it all out there and say that if you're buying only one large expansion, get Dunwich. If you're getting more than one at once, any combination will do.
Dunwich's Tasks and Missions don't come into play too often and the Missions in particular are very rarely followed through. But the sub-boss is super cool and the investigators and monsters and ancient ones are all some of the best, in my opinion. Don't forget injury/madness cards!
Kingsport's Epic Battle is phenomenal. The board is great if you're into encounters or if you don't want the board to provide a giant jump in difficulty (the kingsport AOs are nasty though).
Innsmouth's personal stories are all right, but it's the hardest expansion and you should own either Kingsport or Dunwich before owning it.
Dark Pharaoh and King in Yellow both have awesome theme. King in Yellow is definitely harder though, and has a better herald.
Black Goat's difficulty cards can be completely ignored. The best part of the expansion are the corruptions, but they don't come into play all that often, so get this expansion last, or right before Miskatonic.
Lurker has cool components like the gates and the relationship cards. The herald is cool, but it's not a challenge unless you also have Miskatonic's Reckoning cards.
Lasty—Miskatonic is a great expansion, but it is best when saved for when you have a few expansions. It adds the most to big expansions: particularly Dunwich. It adds less to the small-boxes (to King in Yellow it adds practically nothing).
There aren't any expansions that require any others, but Miskatonic adds things to expansions, so you should wait on that one.
Based on what you said you prefer and what you don't care so much about, I think you should get Curse of the Dark Pharaoh and/or King in Yellow for your small box(es). For a large box I'd recommend Dunwich or Kingsport. Dunwich is considered the best and a must-have.
Here's a ruberic I designed for helping to choose when to get Miskatonic:
Start with a value of 5, which represents the Institutions and the Mythos cards, since that's all you can technically use out of the box with only the base game.
If you own Dark Pharaoh (original/revised): +1/+2
If you own King in Yellow: +0
If you own Black Goat of the Woods: +1
If you own Lurker at the Threshold: +2
If you own Dunwich Horror: +6, then +1 for each other expansion you own (besides Miskatonic).
If you own Kingsport Horror: +4, then +1 for each other expansion you own (besides Miskatonic).
If you own Innsmouth Horror: +2, then +1 for each other expansion you own (besides Miskatonic).
You'll note that owning multiple expansions sums to more than the individual expansion on their own. That said, the total score, for owning every expansion and the revised Dark Pharaoh (not original) is
So you can use this rubric to give an estimate to what "percentage" of the expansion's value you're getting.
If you own only Dunwich Horror and Lurker at the Threshold, you'll get:
5+2+6+(1)= 14, which is less than half of the set's value. If you add Kingsport, the total jumps to 21: more than half the set's value and a 50% increase in value.
On the other hand, owning all four small expansions but no board expansions will give a total of 5+2+0+1+2= 10, only a quarter of Miskatonic's full potential.
Personally, I think that individual board expansions are always better to buy than Miskatonic, but if for whatever reason you're getting Miskatonic without first owning all the board expansions, try to shoot for some value above 20.