The original plan in 1993 was to bring Hogan in, give him a world title run as sort of a "welcome back" gift, and then have him put over Bret Hart at SummerSlam to cement the Hitman as a main eventer. Hogan, however, pulled his usual political bullshit and said he didn't want to put Hart over. Since Hogan wrestled less than a half-dozen times for the WWF in his comeback, Vince figured that he didn't need the aggrevation and settled upon the idea for Hogan to lose to Yoko at KotR. It is surprising how Hogan agreed to be so soundly beaten, as well (Yoko kicked out of the legdrop and Bonzaied Hogan a couple of times after the match). I believe there was also some Vince/Hogan animosity over the Zaharian steroid trials, though I'm not sure about the particulars.
I was born in a manger, like that other guy. You know, he wore a hat?
If look at night in-night out quality matches, I think HBK's first run has to be considered. It really held the WWF together during it's most trying times. Shane Douglas's second run (4-94/4-95)as ECW champ is also one of my favorites.