Captain America and Batman's fight was originally planned to go to completion. Cap would've won, after a while. In the actual book, they spar for a few moments before calling it off, with Batman admitting that Cap could win, after a long time.
When the Marvel and DC universes are given a merged history, The Wasp recalls the original proposed storyline (the '80s-era teams battling Kang and the Lord of Time) as a previous meeting of the two teams.
The cover for the third issue, representing every member either team had in its 40+ years of history. 208 characters in total. Perez actually injured his wrist drawing that cover, which delayed the miniseries for about a month.
There's a page where a bunch of DC characters are stacked up against their Marvel characters on various chessboards. If you squint real hard, you can see Death of the Endless face to face with Marvel's Death.
An intentional example, with the various Marvel vs. DC crossovers shown in one panel (like Lobo vs. the Shi'ar Imperial Guard) or only alluded to.
Darkseid with the Infinity Gauntlet alone would've had limitless possibilities.
As great as the miniseries was, the fact it was about specifically those groups meant that other major characters from those universes (such as the JSA, X-Men, Spidey, Daredevil, Teen Titans, New Gods and Fantastic Four) only appeared briefly. Thankfully, those appearances were usually quite awesome. Batman fighting The Punisher (off-panel) and the drug dealers he was shooting up, anyone?
Kurt Busiek said on the DC message boards that his original plan was for the Batman/Captain America fight to play out all the way. Who would have won? Captain America. Bats does state this, but it would take a long, long time.
The original plan for chapter three of the story was that the Justice League would have an adventure with Marvel-style storytelling and the Avengers would have an adventure with DC-style storytelling. Perez would even draw the Avengers in the style of Carmine Infantino and the JLA in the style of Jack Kirby. Ultimately it was decided that this would slow the story down too much and it was discarded.