WCW without Flair:
1988, they struggle for at least a couple years. Dusty probably stays for a little longer, as do the Busters, which I see Dusty trying to make Tully the new guy. It's transparent but he's someone Dusty trusts enough and if he collapses he can just transition back to either himself or, more importantly, Luger. Otherwise it doesn't feel totally unreasonable to bring in Gilbert or Lawler to give them a shot. Maybe the final destruction of the AWA with Larry or Slaughter or something. Top heels would look like the remaining Horsemen, Muta, and Funk while Luger, Steamboat, Sting, and Nikita on the face end. Skyscrapers get their due after some awesome matches with the RNR and probably wind up doing a quiet split, Powers of Pain style. Doom/Skyscrapers becomes a money hoss fight but there's no way either or both don't jump to the WWF first chance. Sting won't break out nearly as fast but will probably get Luger's midcard run, ending with him being huge and their Warrior. If the chain command still has Herd and Watts, it all doesn't matter. Unless you bring Watts in right after Flair leaves while there's still a chance of his style working well enough. Pillman's push probably goes similarly to how it would, maybe leading to him and Zenk teaming up early for some swank Midnights matches. Ideally as well Heyman would start to get a little more influence during the flux, as well. Flair likely returns when his deal is up anyway, meaning he'd get a depleted and unhappy roster in 1991 or so and be jerked around and basically redo a lot of what he'd have missed. He also probably doesn't get as behind Sting after a run where he'd have to have worked Warrior and judge him a little harsher for unfair reasons.
WWF with Flair:
Only call that makes any sense is calling an immediate audible and having him get Rude's spot with Jake and moving Rude to Warrior sooner. Pair Flair and Heenan, it's an easier transition. Otherwise, you put him with Warrior or Beefcake, and while both are not ideal they were both solid upper carders. There is no way to avoid having him interact with the Mega Powers but it might need to be tried solely because he would throw a huge wrench in that story. Flair is literally the perfect enemy for both of them and could take a lot of heat from them as a result.* Hogan/Flair should be Wrestlemania 6 and Savage/Warrior should be just behind it, ideally meaning the next year actually sells out the Colisseum for Hogan/Warrior. Flair then can do shit with Bossman or something until he leaves, like Rude insulted his momma but Flair fucked her or something. The problem is that Flair could completely overshadow Rude, Perfect, and Dibiase right out of the gate, and while those dudes as Heenan's Horsemen sounds awesome I don't know if it would help or hurt those involved. When the WCW roster raid kicks off and guys like the Skyscrapers, LOD, and maybe Windham jump it just takes up more spots. Flair would jump back like he did in reality, but given how different the dynamics would be vs 1992 I could see him taking a few people with him just based on how things are. Harts, Rockers, Martel-- workrate guys who weren't as appreciated. Flair politically might not gel with 80s Hogan for long and I don't trust Hogan to not fuck him over. Guys like that leaving before the impending steroid problems, leaving most of the roster giant roid monkeys and not normal looking guys, makes the WWF look worse.
*Flair coming out at Wrestlemania and escorting Liz away during the final stretch of the match would've ruled though.