Jean Grey, during periods when she has been rendered temporarily dead or otherwise unusable, has been substituted numerous times, most notably by her Alterniverse daughter, Rachel. Now we currently have Hope Summers, the first mutant born after the Decimation events. She looks like a teenaged Jean, wears the same colors as she had, and displays similar Phoenix-like powers.
And once Hope's storyline needed reason to exist was over, she was taken out of the main books to reunite with her adopted father Cable, and in her place is now the Teenaged, time-lost Jean Grey. She's a 16 year old girl raised in a different time (this time though, the past) who has the traditional Jean Grey look, has a similar personalityand tendency to be a brat, has a lot of story focus with a big bulk of the current conflict in the books revolving around her presence, and is slowly learning just how powerful she is. In short, Jean Grey is the Suspiciously Similar Substitute to her ownSuspiciously Similar Substitute.
As a long-running tradition, the team roster always has to include one plucky, Badass Adorable teenage girl who adopts Wolverine as a Big Brother Mentor. When the character grows out of the role, she's always replaced by another one. Kitty Pryde started the tradition, and her replacements have included Rogue, Jubilee, Marrow, Armor, Pixie, X-23, and most recently Oya. Marrow shook up the tradition a bit by having Gambit as her mentor instead, but the writers cut out the middleman with X-23 by making her Wolverine's female clone (the closest thing to an actual little sister Wolvie's ever going to get).
The character of Tempus introduced in the latest volume of Uncanny X-Men has a strikingly similar time manipulation power set to an earlier character, Kiden Nixon.
Parodied in The League of Extraordinary Gentlemen: The Black Dossier, where we're told the British Government, in assembling the 1950s League, tried to find substitutes of the entire 1890s League. It didn't work.
W.E. John's Worrals for Mina; Hotspur's Wolf of Kabul for Alan; Peter Brady (TV's first Invisible Man) for Griffin; Professor Grey (from The Beano strip The Iron Fish) for Nemo; and a giant robot called the Iron Warrior (from Thrill Comics) for Hyde.
This went as far as to have Wolf hit on Worrals, when Worrals was openly gay.
The Pre-Crisis version of Jason Todd, who took over the role of Batman's sidekick Robin after Dick Grayson became Nightwing, was a carbon copy of Dick Grayson right down to having a similar origin story (his parents were acrobats murdered by Killer Croc). This was averted with the Post-Crisis version, which revised Jason's origin as a street hoodlum who was picked up by Batman.
Jessica Jones was created by Brian Bendis after Marvel denied him permission to use Spider-Woman in his Alias series. This explains their similar names ("Jessica Jones" and "Jessica Drew") and backgrounds (washed up former superheroes who became private investigators).
When Grant Morrison was writing JLA, he was unable to use Hawkman because the character's Continuity Snarl had become such a problem. Instead, he created the replacement character Zauriel. He even hangs a lampshade on it by having Aquaman briefly mistake Zauriel for Hawkman in his first appearance.
Many fans have accused Marvel of doing this with The Inhumans, who saw a complete overhaul in Inhumanity. They now bear a number of resemblances to the mutants from the X-Men franchise. They are ordinary civilians who find out that they are a minority (though not as rare as mutants), have powers thrust upon them, and are a part of a larger conflict, and many are hated for being different and are considered freaks. Even longtime X-Men writer Chris Claremont has commented on this, accusing Marvel and Disney of making the Inhumans into mutant Expies to benefit the Marvel Cinematic Universe (which can't use mutants due to rights issues).
Lampshaded in New Avengers. Daredevil was unable to join the team due to his legal problems at the time, so he suggested to Captain America that Echo join in his place. He pointed out that since she has virtually the same skill set and all his knowledge of the Japanese underworld, it'd be the next best thing to actually having him on the team.
In JLA comics, Vibe was a member of the poorly received Detroit League who, like the other newcomers to the team introduced in that run, had a stroke of misfortune or two when the roster needed to be cleared up for a new team. In his case, he died. Later, the Conglomorate, a rival team to the Justice League, is formed, featuring Vibe's identically-powered brother Reverb (as well as Vibe's JL teammate Gypsy). This was written by the same writer who killed off Vibe in the first place; Reverb lacks Vibe's out-there personality and is generally unlikable for the opposite reason.
John Byrne's run on Wonder Woman dumped the supporting cast established by the previous creative team, most notably archaeologist Julia Kapatelis and her daughter Vanessa, in favor of his own creations, most notably archaeologist Helena Sandsmark and her daughter Cassandra.
Lana Lang started her existence blatantly filling the role of Lois Lane when they started telling stories about Superman's childhood as Superboy. Unlike her modern incarnation, she was both the love interest and the nosy inquisitive girl always trying to prove Clark was Superboy.
The early 1960s Doctor Who comics had the Trods, who were a suspiciously similar substitute for the Daleks, who were unusable at the time due to the rights to publish Dalek comics being in the hands of a different company. This was lampshaded when the comics company finally did get the rights to use the Daleks, which they celebrated by having the Daleks massacre the Trods in their first comic appearance.
Following Ultimatum, the X-Men were disbanded and replaced by the new comic 'Ultimate X', featuring James Hudson, the son of Wolverine as the team's "enforcer". Subverted to some extent, in that Hudson is a teenaged boy with healing and the ability to consciously grow metal coating to his bones, while his father was...Wolverine.
Later, when Peter Parker died fighting Norman Osborn, he was replaced by Miles Morales, a young teen with almost identical powers who became the new Spider-Man. To those who were/are critical of him, one of the biggest critiques is that Miles is too similar to Peter, being a science nerd Nice Guy motivated by guilt from not helping when he could (ironically, being that he could have saved Peter, but didn't). However it's established he isn't nearly as smart as Peter, and thus struggles to decipher his webbing formula, and he's since had Divergent Character Evolution to differentiate him from Peter. Really it's only their origins that are similar.
Apparently due to legal issues with former writer Ken Penders, a large cast of characters in Archie Comics' Sonic the Hedgehog have suddenly up and vanished without seemingly even being allowed to name-drop them. Rob o' the Hedge, missing king of Mercia and Robin Hood expy, has been replaced by the exceedingly similar Bow Sparrow. Along with Rob's love interest Mari-An also being replaced another new character, Thorn the Lop (whether Bow and Thorn have the same relationship as Rob and Mari-An did has yet to be confirmed). Time will tell if other Penders characters get similar treatment.
Lucky Luke: In their first appearance The Daltons were actually shot dead by Lucky Luke! Since the characters proved to be very popular Morris brought them back, or rather their nephews, who looked and acted exactly the same and were also four brothers of differing height! So the Daltons we know today are actually copies of the original.
In the second wave, GI Combat replaced Men of War as the military book, though the substitution ends at genre since the books are very different. Men of War is a fairly realistic modern war story, whereas GI Combat splits time between super-commando counter-terrorism (the "Unknown Soldier" segments) and soldiers who get sent back in time and battle dinosaurs.
When the Batgirl mantle was returned to Barbara Gordonfrom Stephanie Brown following Flashpoint, Barbara's personality appeared to shift to be closer to Lighter and Softer Stephanie's, so she was a similar replacement to her replacement's replacement; this was quickly undone by then making Batgirl full of angst, which helps differentiate it from Steph's book. Stephanie was later slated to appear in the Smallville comic, but editorial ordered her to be replaced last-minute. Now we have a Barbara Gordon in that universe who also acts more like Stephanie would.
This has became worse now that the book is getting a new Creative Team, focusing on Lighter and Softer, complete with a fun redesign and new attitude. While generally accepted, a lot of people have noted that the new take doesn't really fit Barbara Gordon, at least not after what she's been through recently, and actually fits Steph a whole lot better. Pretty much everything, from the costume to the tone of the art revealed to Barbara's entire outlook resembles what one would expect of Stephanie Brown, and thanks to the art style making Barbara look younger, almost turns Barbara into an expy of Steph. Cameron Stewart has stated this is unintentional, as he's neither read Steph's series nor is he overly familiar with her character, and is just basing Barbara's character off of how he sees what Batgirl is supposed to be like.
Dynamite's miniseries Chaos is intended as a revival and reboot of Chaos! Comics from the '90s, reintroducing the flagship characters of that company in a single story that lays out a new continuity. The problem is, Chaos! Comics' most popular character Lady Death isn't available due to the character belonging to another company. Enter Lady Hel.
Medieval Spawn and his angelic opponent Angela were co-created by Neil Gaiman and it was ruled in court that he co-owned the characters with Todd MacFarlane. MacFarlane subsequently created Dark Ages Spawn and the angels Domina and Tiffany. This did not go down well.