Assuming I can't sign guys who didn't get signed and have to work with the people that were actually there...
The biggest blunder IMO was at the very start, announcing Shane had bought WCW, which instantly overshadowed any WWF vs. WCW rivalry by turning it into an extension of the McMahon family feud. On the last Nitro I would have had the announcers not mention WWF at all, just selling the fact that WCW's future was uncertain and that the company was going dark for a while to reboot but would be back soon. Book the show to align with whatever the current storylines were at the time, no "final matches" between Sting-Flair, etc.
Beyond the Shane buys WCW stuff, I thought WWF handled the actual Invasion part well at the beginning. The random run-ins of guys like Booker T felt real. I think making it feel real like when Hall/Nash debuted in WCW as outsiders is the right way to do it. Make it really feel like WCW wrestlers are invading and aren't supposed to be there.
Keep that going for a few months, where renegade WCW guys keep debuting in various matches. THEN you can reveal who has been funding WCW, maybe Shane (would be great if it was Flair, but again I'm working under the assumption I can't use anyone who wasn't in the original) and let WCW take over Smackdown. Run WWF Monday Night Raw and WCW Thursday Nitro independent of each other for about six months, let the WWF audience familiarize itself with the roster, then you can maybe build to a WWF vs. WCW Survivor Series type PPV.
I don't think the Invasion ever needed to "end" though.. like why kill off WCW? Its a proven money making brand. And if you can keep the brands apart long enough to get some of the big names back (Goldberg/Steiner/Sting/Flair) it would have been an even bigger deal when they finally collided.
