-Jericho was never supposed to face Hogan at Wrestlemania 25. They tried to get Hogan/Austin going one last time but Austin refused again since he was dead set on never wrestling Hogan by that point. They wanted Hogan to put over Cena too, but Hogan's doctors screwed up his back surgery and made it impossible for him to compete by the time Mania rolled around (at least according to Hogan... take it with a grain of salt.) Speaking of WM25, Cena and Batista were supposed to have their big rematch from the previous year's Summerslam here, but Batista was too hurt to compete.
-Eddie Guerrero/Shawn Michaels were supposed to have an inter-promotional match at Wrestlemania 22 (which would have been their first ever encounter) but Eddie's passing rendered this impossible, of course. At the same event, Bret Hart was originally planned to fight McMahon but he backed out of it for some reason. Undertaker and Kurt Angle were supposed to battle for the WHC there as well, but Vince split them apart and booked them in different matches instead since he wanted the Streak and the World Heavyweight Championship to act as two separate draws for the event. (Obviously, he changed his mind on that for the next two Wrestlemanias since Taker fought for the WHC at both events, but then he had Donald Trump and Floyd Mayweather to draw big for those events too, unlike WM22, which had no big celebrity to bring in extra buys.) They tried getting Austin/Hogan going here too, but Austin refused.
-Stephanie was supposed to have her very own "Kiss My Ass" club back around 2002-2003 when she was Smackdown GM but she backed out of it.
-Austin was supposed to remain a heel and world champion after the Alliance invasion storyline came to an end at Survivor Series 2001 and keep the title until he dropped it to HHH at Wrestlemania X-8 and then turned back babyface afterwards. Austin wanted to turn back face immediately though, and so plans shifted to him against Chris Benoit at WM X-8 instead, but Benoit still wasn't cleared to compete and so Austin was stuck with Scott Hall instead.
-Goldberg/Rock was originally booked for Wrestlemania X-9 instead of Backlash the next month, but Goldberg didn't in time for that to happen. At the same event, Austin would have wrestled Triple H for the WHC (there were a couple of seeds planted for this match, actually.)
-The long-term idea for Wrestlemania 21 (for about a year) was Cena defeating Brock Lesnar for the WWE Championship and Randy Orton defeating Triple H for the World Heavyweight Championship. They always had Cena and Orton pinned down as their next two breakout stars and WM21 was supposed to the big breakout moment for both of them. But Lesnar walked out after WMXX and JBL took his place instead. And Orton? Well, they rushed his babyface turn and him being booted from Evolution WAY too early, and on top of that, the fans just didn't care for a babyface Orton (although the mishandling of his storyline probably played a hand in that.) And then the fans started to organically get behind Batista as the man they wanted to see dethrone HHH instead, and so Batista got Orton's spot at Mania instead.
Plenty of others I can think of, but I don't want to ramble for too long in one post (wait, too late for that.)
