Most of the complaints here apply to just about every junkyard I've ever dealt with, hardly limited to just LKQ.
I share the frustration with cut harnesses, broken whatever's that just happen to be a part you need, sliced pipes that seemed to have no reason to have been cut, but like what others have pointed out, if you're buying an engine, you're getting the engine, meaning the block, heads, maybe the manifold(s), intake, etc. Any of the accessories or peripherals, consider those as a bonus if they are there and useable. And most places, at least the ones I deal with, charge you extra for those, unless you're buying a fully dressed transplant, which they charge significantly more for anyway.
If you've seen how many yards remove engines or trannys, you'd understand how and why things get sliced and diced the way so many are. Give one of the field monkeys a list of ten cars you need the engines out of, and he's got to have them all ready three hours from now, you aren't going to get every nut and bolt bagged and tagged, every hose clamp removed with decent useable hoses intact, and harnesses daintily disconnected and zip tied out of the way and clean and useable, etc.
Climb under the car, sawzall the converter(s) out. Zap the subframe bolts/nuts off with an impact, then remove the strut bolts and nuts. Hop on the forklift, and start to lift the body off the subframe. Raise it up a bit, anything connected between the engine and body gets sawzall'd. Ka-chunk, subframe and engine/tranny thud onto the ground. Use the forklift to move the chassis out of the way, then zap the engine mount bolts/nuts off, zap the transmission to engine block bolts, chop the harness(s), separate the engine from the tranny, wrap a chain around the engine, use the forklift to move the engine up to the side of the shop outside where it waits for the customer. Watched the process too many times, same way every time. If you want things not chopped and diced, you can go out to the yard and use your own tools and one of the big, moveable cranes available in the yard and have at it yourself. It will take you a few hours, but you'll get everything you want, the way you want it.
Or you can pay them to do the same, but many, at least the ones I deal with, charge shop rates to do it. And I don't blame them.
This is just my experience with parts places. I'm sure it varies depending where you are. This thread just seemed like its directed toward LQK, and I found it a bit strange since it pretty much describes just about every yard around my neck of the woods (PS.. I have nothing to do with LQK, other than visiting the one near my work when necessary. I don't work for them, I don't know anyone who does. I work in aviation myself).