I saw a thread on Reddit and thought to post the same here. Go!
For continuity's sake, Captain America is the first hero. Then Supes and Bats.
Darkseid goes. Thanos stays. He fights Nekron for Death.
Doom (Science/Latveria) versus Black Adam (Magic/Khandaq).
Brave and the Bold miniseries: Nova and Green Lantern.
The Star Sapphires are based out of Themyscira.
AIM and Hydra stay. Marvel has great henchmen/organizations. Kobra, Cadmus, etc. are out. DC never uses their grand-scale organizations in print well at all. Although, they are now building up ARGUS in Justice League and NOWHERE as well. Anyway, Amanda Waller's mission in life is to run counter-terrorism against them.
Matt Murdock is DA of Gotham.
Dr. Strange leads Justice League: Dark. Get Constantine out of there. Keep him in his monthly from Vertigo, but add in Ralph Dibney and Det. Chimp as a supporting cast in the mix to tie it to the universe.
Mxyzptlk is now in the Wonder Woman mythos.
Merge Brainiac and The Leader's origin.
The Riddler v. Reed Richards.
Doomsday? I'm tired of his bullshit. Out.
The Losers join SHIELD.
Hope is a Blue Lantern.
The Flash stays. Quicksilver is out.
Earth-2 is home to the JSA and the Ultimate Universe.
Booster Gold and Cable team-up in a monthly book.
OMAC v. Hulk.
The Hellfire Club (Metropolis) v. the Court of Owls (Gotham). They are both pwned by The Black Glove.
The Brotherhood of Evil Mutants: Toad, Mystique, Blob, Pyro, Avalance, Destiny, Terra, and Beast Boy.
Kamandi is the lead character in Age of Apocalypse.
Magneto and the Metal Men (not corny). 'Nuff said.
Arkham Asylum's warden is Luke Cage.
Mitchell Hundred (Ex Machina) is President.
Batman Inc / Bruce Wayne versus Oscorp and the Thunderbolts.
There's room in the ocean for both Namor and Aquaman. But, mother of god, take the wings off of his feet, though.
The Shi'Ar are out. They are replaced with the Legion of SH relative to their relationship with the X-Men.
Also, Before Watchmen is retconned until proven awesome.
Damien Wayne v. Franklin Richards.
Krona sees the origin of the Universe and awakens the Celestials.
Gorilla City does not exist. Grodd overtakes Wakanda from Black Panther and his son, Batwing.
Neron is out. Mephisto stays.
Phantom Zone and Negative Zone merges.
EDIT - I only read DC books. I hope I didn't offend any Marvel fans when putting this together. I love your universe and characters, but my wallet can only stomach one company every Wednesday.