A few things I can think of...
1. WWF had a much better production team. It seems like the WWF had better audio and video for their shows. The WWF stuff usually looked and sounded crisper. The camera crew got better shots of the action and it looked more professional. Also, the WWF did a better job of putting together video packages to introduce or hype their big shows or feuds. Take a look at the WrestleMania 12, 13, and 14 video packages and the Bret/Shawn build-up video for their iron-man match. The SummerSlam '97 PPV intro was very good. How about the Highway to Hell video package for Austin/Undertaker at SummerSlam '98? What about the WrestleMania 17 intro video and then the Rock/Austin hype video? Nothing WCW put out can compare to these video packages. I'd say WWF really found their stride with this stuff in 1996. When WCW tried putting out video packages to hype upcoming PPV events they always looked cheap and rushed.
2. WWF had better matches. NWA and WWF in the '80s were pretty even when it came to match quality. In the '90s the WWF took it hands down when it came to the number of great matches they put out. I'd say NWA/WCW loses points for relying too much on hokey finishes that never really gave the fans a clear-cut winner. Starrcade '84 ended by referee stoppage by a former boxer with 0 wrestling experience (or refereeing experience for that matter), leaving the fans feeling cheated. Starrcade '86 ended with a double disqualification. This is how you finish the biggest show of the year for the company? What about Hulk Hogan vs. The Butcher in the main event of Starrcade '94? Although some fans place greater emphasis on promos, most still want to see good quality matches and legit finishes that declare a winner.
3. Jim Johnston. The music composer for the WWF put together so many classic entrance songs for the wrestlers. Sure, WCW had some good ones, but their list is not going to touch what Johnston put out for the WWF talent. You know when guys like Hulk Hogan, Bret Hart, Shawn Michaels, The Undertaker, Stone Cold Steve Austin, and The Rock are about to walk out, because their music was so well made. Oftentimes, you would hear a WCW entrance theme start and you would have to sit there for a few seconds to figure out whose music it was. Even when you knew whose music it was it did not pump you up for their entrance like those WWF superstars did. I will give WCW credit for the Hulk Hogan (American Made), Sting (Crow), Goldberg, NWO, and Wolfpack entrance themes though. Those were good. They basically gave Bret Hart elevator music for his WCW entrance theme. Compare his WCW theme to his WWF theme. Night and day as far as what is memorable and will pump you up for the match.
4. WWF took the time to build up angles and feuds, while WCW seemed to rush things. WWF would spend 2-3 months building for a big angle, while WCW would just throw something together 2 weeks before a big show. WCW did do a great job with the NWO takeover and the Hogan/Sting build for Starrcade, but then there was the botched finish to the match and the match was not even good. Also, too many times there would be wrestlers brawling in the ring at the end of Nitro and the last thing you could hear as they went off the air was Tony Schiavone telling you "We're out of time, we'll see you next week" as Sting is hitting someone with a Stinger Splash. In WWF, Stone Cold would clear the ring and they would end the show with him drinking some beer in the ring. It allowed you to see it through to the end.
5. WWF had a mix of more established main eventers (Bret Hart, Shawn Michaels, & The Undertaker), while building newer guys to the main event scene (Stone Cold Steve Austin, Mankind, Kane, The Rock, Triple H, & Kurt Angle). WCW relied on old WCW talent (Flair, Luger, & Sting) or old WWF guys (Hogan, Savage, Hall, & Nash) to cover their main events. WCW also neglected guys like Chris Benoit, Chris Jericho, and Eddie Guerrero, who would later do very well in the WWF. Props to WCW for Goldberg and Diamond Dallas Page though. They just needed to build more substance to Goldberg for after his undefeated streak came to an end. Also, Page was already in his early 40s by the time he reached main event level. They needed younger guys who could capture the attention of the audience for years to come. WWF just did a better job of building stars, going back to the '80s with Hogan, Savage, Warrior, Piper, etc.