I think it's fair to say that the WCW/ECW alliance roster was treated poorly and buried - with possible exception to Stone Cold, RVD, Booker.T (and later, Kurt Angle).
I was so excited when Booker.T started showing up on WWF programming because I really thought it was going to be something tremendously special: WCW invading ECW! The night that ECW arrived (originally to "save" the WWF against WCW), I was amped up to say the least. ECW coming through the crowd gave you that "Shit's about to go down!" feeling. In the end, shit did go down, but not in a good way. It kind of slid down the bathroom wall ever so slowly, so that by the end of the angle every one had smelt it and had enough.
The ECW troops get into the ring and shake hands with the WCW guys - but what really threw me off was when Paul E announced Stephanie McMahon as the new "owner" of ECW. Why?
Well, I know why; because the idea was to get the whole 'Shane & Stephanie are going to overrun Vince' thing happening... but as someone who watched the old ECW, why was this happening? Why was Stephanie just randomly all of a sudden the new "owner"? Bit of an anti-climax. At the very least, I was hoping that Paul E would start off as the owner and then it would later develop on-screen over weeks/months that Stephanie was in control... I mean, we knew the story behind Shane and WCW.
So Booker.T was in. DDP was in. Chris Kanyon was in... and Shane Helms, Billy Kidman, Mike Awesome (yada yada) - but where the hell is Hollywood Hogan or Nash or Hall or Goldberg? Sting was nowhere to be found either. Not Luger, nor Savage. That's when it got sour on me, really. I mean, they had Bagwell in for like 5 minutes, but no cigar there.
The thing about that was, there were really only two standout WCW guys there the whole time. If you didn't really watch WCW back then, you'd still realize: "Hey that's Booker.T/DDP from WCW!"
The Undertaker/DDP/Sara "stalking" angle was interesting to begin with, but they basically just buried Page for the benefit of the whole 'Brothers of Destruction' thing.
Another bad thing about the WCW-side of the roster was the lack of potential defectors like Benoit, Guerrero, Saturn and Malenko. Those were actually former-WCW guys who would've fit a lot more solidly into the mix I think.
ECW had more potential at first, in my opinion. I always thought ECW (as it was obviously not built-up enough to be considered a solid #2) could've played a much better 'mafia' kind of deal. Like hired hands almost. I got the feeling that's the way they were brought in anyway. As troops. Maybe they could've done a more extensive and intriguing wild-card thing with the ECW boys. It would've kept people a lot more interested.
They kind of did something like that with Van Dam. Towards the Survivor Series, somebody was going to jump-ship to the WWF and you got the feeling that it was going to be Van Dam. It also happened with Austin a little bit as well. I was glad to see guys like Lance Storm, Rhyno, Raven, RVD (among others) get exposure on WWF TV. Lance had some real solid matches, including with Edge at SummerSlam 2001 for the IC title. I've always been a big Rhyno mark and RVD was absolutely outstanding for the entire InVasion angle. I was marking for the Dudleyz and Rhyno and Raven and the others jump back to ECW. I thought it's what they really needed for a boost.
Steve Austin, the biggest WWF superstar at the time (considering that The Rock was out in Hollywood at the angle's inception) jumps to the alliance? Are you kidding me? Okay, shocking. But it was only a few weeks back that Austin came out and handed the invaders their asses in a hand basket. So now Austin's on team WCW? I was scratching my head. Austin was fired over the phone by Bischoff and even though Bisch wasn't a part of the angle, it was the dumbest thing to have Austin jump from the get-go.
Kronik would've been an awesome addition for the alliance, had they stuck around. Personal opinion. I thought Stevie Richards as their insane manager was awesome.
The Rock and Jericho's feud at the time of that angle was one of the best things going. I loved Jericho's push. He deserved it too and I think it was also cunning (in a good way) that they never had him jump-ship, even though you kind of felt like he might.
Kurt Angle being the "mystery" WWF defect? Big mistake. Angle and Austin had one hell of a match at SummerSlam for the WWF title. Angle also won the title back in his hometown and that was a glorious thing for the WWF - but he's the fellow who jumps to the alliance? I thought he'd been jealous that Austin was Vince's "new best friend"? Well, Austin was in the alliance and Kurt followed suit... That was just wrong.
The shit that they dragged The Rock through after his main thing with Booker.T was also boring as hell. I think this was before the feud with Jericho, and they had him in all these handicap matches and just really lackluster situations.
Anyway, the Alliance angle wasn't as bad as people often say it is. I was in my "big wrestling fan" stage back then and often go back and watch the old VHS's that I have from 1997-2002 since I used to tape all the shows. It did suck to an enth degree and some of it made absolutely no sense, but there was good and bad and it was (in my opinion) definitely better than anything from 2006 onwards.
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Honorable Mentions:
RVD vs Jeff Hardy (SummerSlam 2001; Hardcore Ladder Match)
Angle vs Austin (SummerSlam 2001)
The Rock/Jericho Feud
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Downsides:
William Regal's utterly useless defection, only to become the WCW Commissioner
The "Stephanie slapped Linda" issue leading up to the Survivor Series
WWF defectors being bigger than the actual invaders and the misuse of the WCW/ECW locker in general