I did some research and here's what I found:
*Christian originally slated to be Jeff Hardy's attacker back in 2009.
*Kurt Angle originally slated to win the Undisputed Title at Vengeance 2001.
*Matt Hardy proposed an "Angelic Diablo" gimmick for his return from injury before his release around the Edge-Lita scandal.
*Kane/Rey in 2008 was actually supposed to be Kane returning with the mask.
*Batista vs Mohammed Hassan for Summerslam 2005 was originally supposed to have Hassan winning the WHC. Of course, he was fired before this could happen.
*Jericho originally planned to face a big time legend at Wrestlemania 25, rumoured to be Hulk Hogan or even Steve Austin.
*Cena vs Michaels at WM 23 was supposed to be Cena vs HHH but HHH got injured against Rated RKO the previous December.
*Lex Luger was supposed to win the WWF title at WM 10 but due to lack of popularity they put Bret Hart over instead (one internet rumor was that Bret refused to let Lex go over and threatened to walk out but neither party gave any hint that that was true)
*Ahmed vs. Farooq was supposed to happen at Summer Slam 1996 (they had graphics etc.) but then Ahmed got a legit kidney injury.
*Brutus "The Barber" Beefcake was supposed to win the Intercontinental Title from The Honky Tonk Man at SummerSlam 1988, but the writers felt that he hadn't been getting over on his face push and instead gave it to The Ultimate Warrior, changing the storyline less than 3 weeks before the PPV. He was then written in again to win the Intercontinental Title at SummerSlam 1990 from Mr. Perfect (Brutus was the first person to pin Curt Hennig in the WWF ending his streak), but just before the PPV he was involved in a parasailing accident requiring 9 hours of surgery to completely reconstruct his face and was out of wrestling for around 3 years. Instead the title went to "The Texas Tornado" Kerry Von Erich.
*Apparently, Bret Hart and Hulk Hogan were supposed to face each other at Summerslam 93 but Hogan refused to lose to him because apparently he was ''too small'' and lost the belt to Yokozuna instead.
*A young Rocky Maivia was going to work a program with Shawn Michaels and HBK, being the ego maniac he was back then (and still is today in a way) refused to work with the young Rocky.
*If Owen didn't fall to his death when he did he was meant to get the "Game" gimmick that Triple H had throughout his entire career and pretty much everything Triple H now was meant to be him, leaving Triple H to recieve it as a fluke.
*The Wrestlemania 18 main events were planned to be totally different. The original plan was Austin vs Rock in a rematch from Mania 17 with Austin as the heel.However after HHH got injured they wanted heel Austin vs babyface HHH as the main event and Austin vs Rock at Summerslam (which then never took place). Problem now was that Austin refused to stay heel until Mania and drop the title to HHH.So now they needed a new heel champ to face HHH. They decided to give Angle the belt until a few days prior to Vengeance when Vince decided to push Y2J instead and give him the title and so it ended up being Y2J vs HHH. This left Austin and Rock with no opponents again so they planned to have the rematch between those two (face vs face) just without the title on the line. This plan changed however when they brought in the NWO.
*Obviously feeling Austin vs Hogan or Rock vs Hogan would be a bigger draw than the rematch between Austin and Rock they approached Austin with the idea to wrestle Hogan which he declined. So they went with Rock vs Hogan.
*Lesnar/Austin was supposed to happen at Wrestlemania 19, but Austin didn't want to put Lesnar over. Definitely changed for the better for both men that night.
* Shawn Micheals Vs John Cena was actually set to continue well beyond backlash. The Cena/Khali fued was there to allow Cena/Micheals fued to take a break with HBK coming back and take the title off Cena. But Shawn decides to take sometime off and plan were change. They ended up doing a HBK beat John Cena in a 1 hour match.
*Big Show was chasing Chris Masters (when Master was still having his big push) to take on his Master Lock challenge. But after 3 weeks, the feud was dropped.
*A member of the WWE SmackDown creative team pitched an angle for the Dolph Ziggler and Maria storyline which would have had Ziggler blackmailing Maria with video footage. It would have been heavily implied that the footage was a sex tape, although they never would have come right out and said it.The proposed angle called for Ziggler threatening that he would show it to her family and friends, but not any of the fans. The angle was rejected.
*Booker T once recieved a note:"I still remember"
*A match between Umaga & Jackass was once planned.
*Before the unveiling of Hornswoggle as 'Vinces son' just over a year ago the planned storyline was actually to have Mr Kennedy be the 'illigitimate Mcmahon'. In this scenario Kennedy would be embraced by Vince as his son and head in to a feud with Shane and then HHH, for this WWE would actually acknowledge on screen that Stephanie and HHH are married and the two would be a couple on tv. This may have even led to a feud between the two over the WWE title.