My view of replacing Peter Parker in the Ultimate Universe is this;
The Ultimate Universe has been decimated recently. Look at the list of dead characters *SPOILERS IN CASE*
Angel (Worthington III, Warren) - dead
Beast (McCoy, Henry "Hank") - dead
Ben Parker (dead)
Bishop - dead
Blob (real name Fred J. Dukes) - dead
Cannonball (Guthrie, Sam) - dead
Captain America (Rogers, Steve) -dead
Captain Britain (Braddock, Brian) - dead
Captain France (Etherlinck, Hugo) - dead
Captain Italy (Landi, Umberto) - dead
Captain Spain (Fraile, Carlos) - dead
Carnage - dead
Cyclops - dead
Daredevil (Murdock, Matthew "Matt") - dead
Dazzler (Blaire, Allison "Ali") - dead
Deathstrike (Oyama, Yuriko) - dead
Detonator (Gibson, Ricky) - dead
Diablo (Esteban Corazon de Ablo) - dead
Doctor Doom (Van Damme, Victor)- dead
Doctor Strange (Strange, Stephen Junior) - dead
Emma Frost - dead
Enchantress- dead
Fenris (von Strucker, Andrea and Andreas) - dead
Forge (unknown) - dead
Gambit (LeBeau, Remy) - dead
Giant Man / Ant Man / Yellowjacket (Pym, Henry "Hank") - dead
Green Goblin (Osborn, Norman) - dead
Hard-Drive (unknown) - dead
Hobgoblin (Osborn, Harry) - dead
Hurricane (unknown)- dead
John Stacy - dead
Jarvis, Edwin - dead
Jeanne de Wolfe - dead
Juggernaut (Marko, Cain) - dead
Justin Hammer - dead
Kingpin (Fisk, Wilson) - dead
Kaine - dead
Magneto (Lensherr, Erik)- dead
Multiple Man (Madrox, James) - dead
Nightcrawler (Wagner, Kurt)- dead
Nihil - dead
Malachi "The Jellyfish" Kelly - dead
Polaris (Dane, Lorna)(dead)
Proteus (Xavier, David) (dead)
Quicksilver (Lensherr, Pietro) -Dead- Now currently alive.
Red Skull - dead
Scorpion (clone of Peter Parker)(Real name is Mac Gargan) - dead
Sebastian Shaw - dead
Tarantula-dead
Unus (unknown) - dead
Wolverine (Howlett, James "Logan") - dead
Professor X (Xavier, Charles) - dead
Yellowjacket (Ultron) - dead
And after all of that, they have then killed off Peter Parker and replaced him with Miles Morales.. To be honest.. who cares. The Ultimate universe is now so far away from 616 that i cant see that it now matters anymore.