I prefer the theatrical versions. Though I own both the 2-Disc Special Editions and the Blu-ray's.
Well I haven't seen TMP's theatrical version for years now so I can't compare with the one I have, but I prefer TWOK's special edition because there's some added character moments that I feel are missing from the theatrical cut.
I think those extra scenes kill the pacing of The Wrath of Khan
. I remember watching the theatrical cut the first time on Blu-ray (first time I had seen the theatrical version in years) and thinking how crisp it was compared to the Director's Edition.
But, everyone has different things that they look for in a film.