I had very similar experiences on El Al flying from ORD to TLV and back. While security personnel in TLV was very polite and courteous, it took them 2 and a half hours to process me. They checked absolutely everything, I was in the back room, and as a result, missed my flight. They put me on a later flight departing in an hour, middle seat... A lot of inconvenience, but at least I was dealing with smart and courteous people the entire time.
Flying from ORD to TLV it took them also about 2 and a hald hours to process me, however the personnel was very rude. I would say it was the rudest security/check in experience I have ever had. As a result, also a middle seat and almost late for my plane.
Result here is that I will not fly El Al to Israel again. Flying from Israel, everyone goes through the security process, so El Al is not an issue here, but overall, I will stick with SkyTeam.
I agree, i would rather deal with our morons at TSA than Israeli style security, although I have to say that their TLV security is top notch and very professional, at least i didn't feel like they were treating me like a child.