The most obvious differences would be that 199999 lacks all of the characters whose movie rights are owned by other studios instead of Marvel, and thus will never show up in the 199999 universe despite existing in 1610 so long as other studios hold the rights. While the exact details of the movie right deals have never been revealed, a number of people supposedly "in the know" have said that the rights are renewed so long as the studios continue to actively develop movies for each character. So, so long as Fox continues to work on X-Men or Spider-Man movies, Fox will continue to own the rights - blocking Marvel from using their own characters in the 199999 universe.
Of course with the lack of these characters existing, their back-stories and interactions also never existed.
Screenrant lists the movie rights as the following (Note that not all of the characters listed below exist in the Ultimate/1610 universe - I'm just copy/pasting to be complete):
20th Century Fox
- Daredevil: Daredevil/Matt Murdock, Elektra (Natchios), The Kingpin/Wilson Fisk, Bullseye, Jack Murdock, Karen Page, Ben Urich
- Elektra: Christine Cord/Tatoo, Typhoid Mary/Marry Alice Walker, Kirigi, Stick, Stone [UPDATE: As of April 2013, the Daredevil/Elektra rights have reverted to Marvel]
- Fantastic Four: Doctor Doom/Victor von Doom, Human Torch/Johnny Storm, Invisible Woman/Susan Storm, Mr. Fantastic/Dr. Reed Richards, The Thing/Ben Grimm, Nova/Frankie Raye, Alicia Masters, Willie Lumpkin
- X-Men (Mutants): [Agent Zero/Maverick/David North], Angel/Warren Worthington III, Arclight/Phillippa Sontag, Beast/Dr. Henry Phillip “Hank” McCoy, [Blob/Frederick J. Dukes], [Bolt/Christopher Bradley], Callisto, Colossus/Piotr Nikolaievitch Rasputin, Cyclops/Scott Summers, [Deadpool/Wade Wilson], Emma (Grace) Frost, Jean Grey/Phoenix, Juggernaut/Cain Marko, Gambit/Remy LeBeau, Glob Herman/Herman Gardner, Iceman/Bobby Drake, Jubilee/Jubilation Lee, Katherine “Kitty” Anne Pryde, [Kestrel/John Wraith], Lady Deathstrike/Yuriko Oyama, Leech, Magneto/Erik Magnus Lehnsherr, Mastermind/Jason (Wyngarde), Multiple Man/James Arthur Madrox, Mystique/Raven Darkholme, Nightcrawler/Kurt Wagner, Phat/William Robert “Billy-Bob” Reilly, Professor Charles Xavier, Psylocke/Elizabeth “Betsy” Braddock, Pyro/St. John Allerdyce, Quill/Max Jordan, Rogue/(Anna) Marie, Sabretooth/Victor Creed, Sebastian Hiram Shaw, [Silver Fox], Siryn/Theresa Rourke Cassidy, (The) Spike, Storm/Ororo Munroe, Wolverine/Logan
- X-Men (Non-Mutants): Non-Mutants: Drake Family (Steven, Madeline, Ronny), Grey Family (Dr. John, Elaine), Henry Peter Gyrich, Robert Edward Kelly, Dr. Moira Kinross MacTaggert, Dr. Kavita Rao, William Stryker, Bolivar Trask, Warren Worthington II
New Line Cinema
- Vampires: Blade, Deacon Frost, Dracula/Vlad Tepes
- Non-Vampires: Hannibal King, Abraham Whistler [UPDATE: Since the time of writing this, The Blade rights have been transferred back into Marvel's hands.]
- Ghost Rider: Ghost Rider/Johnny Blaze, Blackheart/Legion, Phantom Rider/Carter Slade, Abigor, Gressil, Mephistopheles, Wallow, Barton Blaze, Roxanne Simpson [UPDATE: As of May 2013, the Ghost Rider rights have reverted to Marvel.]
- Spider-Man: Spider-Man/Peter Parker, Doctor Octopus/Otto Octavius, Green Goblin/Norman Osborn, (New) Green Goblin/Harry Osborn, [The Lizard]/Dr. Curt Connors, Sandman/Flint Marko, Venom/Eddie Brock Jr., Betty Brant, Dennis Carradine (Buglar), J. Jonah Jameson, Ben Parker, May Parker, John Jameson, Joseph “Robbie” Robertson, Gwen Stacy, Mendel Stromm, Flash Thompson
- Punisher: The Punisher/Frank Castle, Jigsaw/Billy Russoti, Microchip/Linus Liberman, Joan the Mouse, Maginty, Mr. Bumpo, Spacker Dave, The Russian, Maria Elizabeth Castle, Detective Martin Soap [UPDATE: Since the time of writing this, The Punisher rights have been transferred back into Marvel's hands.]