I disagree that it was an accepted practice. I don't know of any technical person who didn't hate them from the very first time they saw one. Remember this was back during dial-up days and you had to wait forever for that crap to load. I can't tell you how many sites I left before ever seeing their content because when I saw flash loading I just switch back to my search engine and find the next link. Heck, I still do that.
edit: I forgot to mention my even bigger gripe about the flash intros, and that was because I was basically being forced to sit through a commercial before I could interact with the company. It went (and goes) against the very basics of web use.
I would say the people defining an accepted practice are the people paying the bills. If the company wanted it, the technical person made it so they would get paid. I would admit it was probably the technical people who finally convinced the majority to abandon them. Plus the fact that over time they could see that the idea was failing them, much like you point out. But until that moment it was accepted practice among major websites. The fact you remember them so vividly in your dislike of them almost proves my point.
But alas, I agree, they were a total waste of time. As I said, the people who pay the bills don't always listen to the people that they should listen to.
edit: I forgot to mention my even bigger gripe about the flash intros, and that was because I was basically being forced to sit through a commercial before I could interact with the company. It went (and goes) against the very basics of web use.