I own DUNWITCH HORROR and DARK PHARAOH but never mixed them up to avoid diluting the theme; is this a legitimate concern or am I nitpicking? I kind of felt that it'd be like watching two movies at once...

 Play them one at a time first.

They're both different experiences. Mixed expansions will give you less of the features of one expansion (usually anyway, though this doesn't apply too much to Kingsport), but will surprise you with certain features of all the expansions mixed in. The difficulty also rises considerably when playing with several mixed expansions, at least according to the statistics page (hope someone gets the link back for that one), though Kiy as a permanent exhibit is pretty tough on its own.

Personally, I love playing with mixed expansions due to the difficulty and the surprise factor, despite there being a strong dilution of Dunwich gates, KiY act cards and exhibit items.

The best games I've played are either with just 1 expansion, or 1 card expansion (CoTDP, KiY, BGotW) plus 1 board expansion (Dunwich, Kingsport).

My group has has great experiences with Dunwich + KiY pairng...Every move tends to count more, creating a really tense game.

I never mixed them up yet, to keep the ambience optimal. I have doubts about the added value of the new extensions in regard to diversity...