Flair vs Savage - It lasted longer, main evented both WM and Starrcade, better matches, more World Title switches.
Hogan vs Savage was good in 86 and the meeting at WM 5 was very well promoted and layed out. Match wise I liked some of their work in 86 better than 89. In WCW other than making Savage job another title to Hogan the fued never really took off, partly because of Savage's injury as well as Hogan's part time wrestling status and heat between them behind the scenes because Hogan would never lose a match to Macho Man.
The build up to Flair/Savage leading in WM 8 was classic, and next to Hogan/Flair this was probably the most talked about Dream Match of the time. Flair's promos were absolutely among his all time best, plus the doctored photos, etc. Flair's phenomenal 62 minute win at Royal Rumble also added to the intrigue.
In WCW you had Flair beatdown Savage's dad twice (once on Fathers Day, then pin Randy to win their match - OUCH!!!), a great match outside at Bash At The Beach (lumberjack match), Savage convincing former Flair valet Woman to join his side vs Horsemen (only to be swerved by her and Flair), then the return of Liz to help Randy (only to swerve him again and help Flair beat him in the Cage at SuperBrawl for the title), then Savage went off the deep end and was suspended for awhile, he was stalking Flair, Flair did those great promos with Liz "Hey, it's on Randy" about living the high life on Savage's credit cards, in fact the whole Catered Ringside Buffett deal with Flair in 96 started in this fued (all on Savage's money Liz stole from him) although they used this set up after the two stopped their fued.
Flair-Hogan was completely messed up in WWE. No one ever says why, although there are theories that Hogan initially wouldn't lose to Flair (the idea of Flair beating Hulk at the Rumble, then losing at WM). Niether man has ever said much, saying it was a management decission. We do know that by 92 the federal steroid investigation was in full swing and WWE was pushing out wrestlers with drug problems as well as those who might be indicted (Piper). Hogan was pushed into a "Retirement Match" vs Sid at WM which sucked, basically just a way to get one last PPV out of Hogan while setting up the return of Ultimate Warrior (which bombed, Warrior really only had one good short run 89-91, he never came close to that ever again).
In WCW at first Hogan-Flair looked really interesting, playing up on the fact that they did wrestle in WWE but with noi clear cut winner (all their matches were count-outs and DQ's). Plus Flair was dominant as WCW champion, having survived Vader, Steamboat, and Rude and he like Hogan was fan favorite. Once they turned Flair heel and had him swerve Sting it became clear Hogan would win outright, a recreation of late 80's Hulkamania vs Horsemen Era Flair. What was worse is that Hogan pretty much dominated everything for the next two years, the fued was very one sided till 96. This was the same problem with Hogan-Savage in 89 - when Savage turned heel and Hogan made his return from extended absence you knew he was going over at WM. The fact he never lost any big matches, not even non title or tag bouts vs Savage made that fued grow real old real quick. Worse, in WCW fans did not want to see Flair humilaited by Hogan. Hogan found he couldn't draw except vs Flair and large portions of the audience wanted him to lose. The NWO and heel turn probably saved Hogan's career at that point, older fans losing interest in his one dimensional matches and newer fans more entertained by the crazy antics of Flair, the womanizing, partying, over the top promos.
Hogan did deliver good matches with Savage in WWE, their handful of WCW matches were not very good. I still take their bouts in 86 over their run in 89, but they were pretty entertaining too. Their WM match was one of the Top 5 matches of Hogan's career. Savage and Flair had very good matches in both companies, particularly WM 8 in 92 and Bash At The Beach 95. Hogan-Flair had good matches in both companies. Their Madison Square Gaden match in 91 was slightly better than their typical house show match, very good. Their best was Bash At The Beach 94, Hogan's initial WCW Title win. The crazy Clash Of Champions Match in Aug 94, their fan favorite Flair vs Hollywood Hogan Clash Match in 96, and SuperBrawl 99 were also good. Their other matches were largely average.
WCW dropped the ball by not going full force with a fan favorite Flair vs Hollywood Hogan run, but then they dropped the ball on a lot of potential money making stuff in the late 90's, much of which has been discussed to death other places on this website.