While Marvel vs. DC was the biggest superhero crossover event of the 90s, the sequel should take zero inspiration from the original - or perhaps Marvel and DC Comics should ignore previous continuity altogether. The landmark event was the result of over a decade of planning and communication difficulties between companies, and the end product was a veritable storm of 90s cliches with very little in the way of lessons learned. The comics industry and the world at large have changed drastically since, which is why the followup to the event must make significant changes.
1996's Marvel vs. DC (two out of four issues were titled DC vs. Marvel in the interest of fairness) began when the two major universes began to influence the other. As the universes began to merge, Marvel character interacted with their DC counterparts: Superman met Spider-Man (in their civilian identities while working for the same newspaper), Wolverine stole Batman's Batmobile, and Robin even found himself teleported to Jubilee's bedroom. Eventually, the source of the incursions was revealed: two celestial "Brothers" who each embodied the two universes encountered one another after eons - and rather than fight directly, they would choose champions from each Earth to fight in their stead.
The remainder of the series consisted of multiple fights between Marvel and DC superheroes, and a fatal flaw presented itself within the writing: the heroes were far too evenly-matched. Superman fought the Hulk (two immensely-powerful characters), Thor fought Captain Marvel (two lightning-wielders with the power of the Gods), speedsters Flash and Quicksilver battled one another and so on. While these fights served to answer fan-favorite "who would win" debates, they were often boring; characters simply attacked each other until one lost.
The right way to craft a sequel to the event is to pit different characters against one another, but this time stack the odds against one of them. Instead of Superman fighting the Hulk, Superman fighting Hawkeye would make for a more interesting fight (Hawkeye is clearly no match for Superman's strength and must find another way to defeat him). Flash cannot be pitted against another speedster, but surely Doctor Strange would know spells that would stop Barry Allen in his tracks. Storm fought Wonder Woman in the original event, but Storm fighting Batman would be far more interesting.
Additionally, many of the fights were decided through a fan vote in the original, but this only led to the more popular characters defeating their stronger opponents (Wolverine inexplicably defeating Lobo is one such example). As enticing as it would be for fans to decide the outcome of the fights, it would hamper the writing team - and again, the outcomes of these battles do not necessarily matter. How a fight is won is exponentially more exciting than whether a fight is won or not, and that is why Marvel and DC Comics should completely ignore the original template of Marvel vs. DC when writing the sequel.
Next: Avengers vs Justice League Expose Marvel & DC's Different Philosophies